Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $77 - Fully Refundable Options

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Our top choices for Southeast Minnesota hotels

A modern dining area with high tables, chairs, and pendant lighting.

A multi-story hotel with a modern design, featuring a prominent entrance with a covered area and a parking lot in front.

A hotel room with two beds, a desk with a computer, a chair, and a window with a view.

A swimming pool with a tiled deck, sun loungers, and a lifeguard chair.

1. Hampton Inn & Suites Rochester-North

Rochester

Mark

CA $144

CA $165 total

includes taxes & fees

Nov 6 - Nov 7

A hotel room with a bed, a desk, a chair, a sofa, and artwork on the walls.

A conference room with round tables and chairs, white walls, and a carpeted floor.

A hotel room with a desk, a television mounted on the wall, a small refrigerator, a microwave, a blue chair, and a door with a mirror.

A gym with treadmills, elliptical machines, and a stationary bike.

2. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Terri

CA $105

CA $121 total

includes taxes & fees

Nov 7 - Nov 8

A spacious outdoor dining area with multiple tables and chairs, large windows, and a wooden ceiling structure.

A reception desk with a modern design, featuring a wooden panel and a wall adorned with framed botanical artwork.

An outdoor dining area with wooden beams, tables, and chairs.

A modern hotel room with a large bed, a sofa, a small table, a desk, and a wardrobe.

3. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

Naomi

CA $144

CA $166 total

includes taxes & fees

Nov 14 - Nov 15

A modern indoor patio with a fire feature, seating, and large windows.

A modern hotel lobby with a large glass wall, a green wall mural, and a seating area with sofas and chairs.

A modern living room with a fireplace, large windows, and a flat-screen TV mounted on the wall.

A modern interior with a seating area, a bookshelf, and a window with a view of trees.

4. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

James

CA $154

CA $196 total

includes taxes & fees

Nov 6 - Nov 7

A hotel reception desk with a wooden counter, a computer, and a vase with flowers.

An indoor swimming pool with wooden beams and white chairs around it.

A hotel room with a large bed, a separate bathroom with a bathtub, and a skylight ceiling.

A living room with stone walls, a fireplace, leather furniture, and a ceiling fan.

5. Baymont by Wyndham Kasson Rochester Area

Kasson

Dana

CA $92

CA $98 total

includes taxes & fees

Nov 1 - Nov 2

A modern hotel lobby with a reception desk, seating area, and a kitchenette.

A hotel with a covered entrance, multiple floors, and a parking lot.

A hotel room with a large bed, a desk, a chair, and a kitchenette.

A modern hotel lobby with a reception desk, seating area, and a large window providing natural light.

6. Spark by Hilton Rochester South

Rochester

Stanton

CA $94

CA $108 total

includes taxes & fees

Nov 1 - Nov 2

A spacious lobby with a reception desk, sofas, and a coffee table.

An indoor swimming pool with clear blue water, surrounded by tiled flooring and equipped with a pool ladder.

A Sleep Inn hotel with a covered entrance, stone pillars, and a clear blue sky.

A lobby with a brown sofa, yellow armchairs, a coffee table, and a clock on the wall.

7. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

CA $107

CA $123 total

includes taxes & fees

Nov 15 - Nov 16

An outdoor seating area with a fire feature, blue cushioned chairs, and a modern building with large windows in the background.

A modern indoor pool area with lounge chairs and a pool.

A modern dining area with round tables and chairs, a large painting on the wall, and a flat-screen TV mounted above a geometric-patterned wall.

A modern bar area with seating and a counter.

8. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Arlan

CA $178

CA $205 total

includes taxes & fees

Nov 13 - Nov 14

A self-service breakfast station with a waffle maker, coffee machines, and a variety of condiments.

A reception area with a wooden reception desk, a red doormat, and framed awards on the wall.

A compact laundry area with a washing machine, dryer, and a water fountain.

A hotel lobby with leather sofas, a stone fireplace, and a patterned carpet.

9. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $92

CA $106 total

includes taxes & fees

Nov 15 - Nov 16

A Holiday Inn Express building with a covered entrance, outdoor seating area, and a well-lit facade.

A coffee station with two espresso machines and a variety of coffee pods and cups.

A hotel lobby with leather armchairs, a fireplace, patterned carpet, and a dining area in the background.

10. Holiday Inn Express & Suites Rochester – Mayo Clinic Area by IHG

Kutzky Park

Janet

CA $141

CA $163 total

includes taxes & fees

Oct 31 - Nov 1

An outdoor seating area with wooden pillars, colorful striped cushions, and potted plants.

A modern hotel room with a bed, desk, and kitchenette.

A modern lounge area with a sofa, chairs, and tables.

A modern restaurant with a counter, seating area, and a TV screen.

11. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

CA $154

CA $177 total

includes taxes & fees

Nov 7 - Nov 8

A restaurant with wooden tables and bar stools, a bar area with a counter, and multiple televisions mounted on the walls.

A bar with wooden stools and a neon sign.

A modern kitchen with wooden cabinets, a microwave, an oven, and a dishwasher.

A hotel room with two beds, a desk, a chair, and a mirror.

12. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

blake

CA $106

CA $122 total

includes taxes & fees

Nov 8 - Nov 9

A modern outdoor seating area with a built-in fireplace, two wooden chairs, a table, and a sofa.

Three exercise balls aligned against a window with a tree view.

A modern bar area with a long counter, bar stools, and a television screen mounted on the wall.

13. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Amanda

CA $147

CA $172 total

includes taxes & fees

Nov 25 - Nov 26

An indoor swimming pool with a curved design, surrounded by palm trees and a white pool ladder.

A hotel room with a large bed, a desk, a chair, and a view of the outdoors through the window.

A modern hotel lobby with a reception desk, a digital information kiosk, and a patterned floor.

A modern hotel with a prominent neon sign, multiple floors, and a well-maintained lawn area.

14. Treasure Island Resort & Casino

Welch

Kristine

CA $117

CA $146 total

includes taxes & fees

Nov 1 - Nov 2

An outdoor patio area with yellow umbrellas, wicker furniture, and a sign for Centerstone Plaza Hotel.

A garden with a water feature, rocks, and yellow umbrellas.

A modern living room with a dark wall, a decorative light fixture, and a patterned wall art piece.

A modern reception area with a wooden reception desk, glass pendant lights, and a long hallway with seating.

15. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Deanna

CA $160

CA $184 total

includes taxes & fees

Oct 31 - Nov 1

A Comfort Inn hotel with a stone facade, a covered entrance, and a parking area.

A modern dining area with wooden tables and chairs, a kitchen with granite countertops, and a view of the outdoors through large windows.

A spacious living room with a stone fireplace, blue sofas, and a flat-screen TV.

A spacious lobby with a central seating area, a reception desk, and a fireplace.

16. Comfort Inn & Suites West - Medical Center

Rochester

Tammy

CA $121

CA $139 total

includes taxes & fees

Nov 15 - Nov 16

A hotel breakfast area with a self-serve station, including a waffle maker, toaster, and various food items.

A compact kitchen with a microwave, refrigerator, and coffee maker. A small bar stool is near the counter.

A hotel lobby with a patterned carpet, two beige armchairs, a small table, a clock, a fire extinguisher, and a staircase.

A hotel room with a large bed, bedside tables, a mirror, and a patterned carpet.

17. Quality Inn & Suites Mayo Clinic Area

Rochester

Jessica

CA $97

CA $113 total

includes taxes & fees

Nov 7 - Nov 8

A hotel room with a large bed, a desk with a computer, a chair, and a TV.

A breakfast bar with a wooden counter, a coffee machine, and a refrigerator.

A modern living room with a stone fireplace, a blue armchair, a round coffee table, and a large window offering a view of the outdoors.

18. Fairfield Inn & Suites Rochester Mayo Clinic Area/St. Marys

Kutzky Park

Brien

CA $163

CA $187 total

includes taxes & fees

Nov 6 - Nov 7

An indoor swimming pool with a dolphin sculpture, wooden ceiling, and clear windows.

A hotel room with a large bed, two bedside tables with lamps, a telephone, and a window with sheer curtains.

A hotel room with a flat-screen TV, a sofa with a red pillow, a small table, and a lamp.

A hotel reception area with a coffee station, seating area, and a fireplace.

19. TownePlace Suites by Marriott Rochester

Rochester

Christina

CA $137

CA $158 total

includes taxes & fees

Nov 6 - Nov 7

A modern hotel lobby with a reception desk, seating area, and a dining space.

A Holiday Inn Express building with a stone facade and illuminated signage.

A modern hotel room with a wooden desk, orange chair, dark sofa, and a small table.

A hotel room with a bed, desk, chair, and a bathroom.

20. Holiday Inn Express Rochester South - Mayo Area by IHG

Rochester

Rick

CA $115

CA $132 total

includes taxes & fees

Nov 7 - Nov 8

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Vacation Rentals in Southeast Minnesota

Aparthotel

A spacious living area with a modern staircase, leather sofas, and contemporary lighting.

An outdoor seating area with blue sofas and wicker chairs, a wooden table, and green ottomans on a tiled patio.

A modern interior with a large dining table, sofas, and a kitchen area.

A modern pool table in a spacious, well-lit room with large windows and a bar area.

The Berkman

Folwell

"Excellent service and wonderful room!"

Apartment

A bedroom with a large bed, a TV on a dresser, and a view of the city through large windows.

A multi-story building with the sign 'Broadway Plaza' indicating a commercial or hotel property.

An indoor swimming pool with a clock on the wall, lounge chairs, and a lifeguard warning sign.

Broadway Plaza, Trademark Collection by Wyndham

Downtown Rochester

"Clean room and great location"

Apartment

A wooden interior with a kitchen, bar area, and a staircase.

A two-story building with a storefront featuring a sign for coffee, ice cream, and craft drinks. There are steps leading to the entrance, a bench outside, and potted plants.

A modern kitchen with stainless steel appliances, wooden cabinets, and a stone tile floor.

A wooden cabin interior with a bed, a ceiling light, and a window.

Lake Pepin Escape: Loft Cottage & Fireplace

Pepin

"Great location and very well furnished with new appliances."

Apartment

A modern kitchen with a central island, bar stools, and a large window.

A spacious living area with a large sofa, a coffee table, and a dining table with chairs. There is a ceiling fan and a floor lamp.

A deck with two wooden chairs and a fire pit.

A marina with boats docked, a parking area, and a view of the surrounding landscape.

1 Block to Lake City Marina: Condo w/ Rooftop Deck

Lake City

"Wonderful property, spacious, well-appointed and comfortable. Would definitely rent again."

Apartment

A bedroom with a bed, a chair, a table, a fireplace, and a ceiling fan.

A wooden deck with Adirondack chairs lined up against a building with a flag.

A single-story house with a front porch, a small staircase leading to a deck, and a stone retaining wall.

A living room with a fireplace, a television mounted above it, and a large window offering a view of the outdoors.

Pet-friendly Wabasha Studio: Boat, Ski & Explore!

Wabasha

"Great property! Very convenient location as well."

Cottage

A modern interior with a stone fireplace, wooden walls, a leather sofa, and a dining area.

A cozy interior with a wooden ceiling, a fireplace, a red sofa, a leather couch, and a foosball table.

A kitchen with wooden cabinets, a stove, a sink, and a window with a view of trees.

A log cabin interior with a wooden ceiling, a red sofa, a brown leather couch, and a person seated on a chair.

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

Pepin

"What a fun place! Plenty of room. We played foosball had a fire outside. We enjoyed the fireplace too. We hadn’t anticipated no TV though. You might want to add that to your description. The water is definitely smelly, so we truly appreciated the 40 bottles of water you provided. Definitely a great place for a girl’s weekend or family reunion!"

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Stay near popular Southeast Minnesota attractions

Villa Bellezza

8.4/10 (31 reviews)

You can enjoy a tasting or tour at Villa Bellezza during your travels to Pepin. While you're in the area, stroll along the lakeside.

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Mayo Civic Center

9.2/10 (818 reviews)

Catch an event at Mayo Civic Center during your trip to Rochester. Attend a sporting event or simply visit the area's shops.

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Apache Mall

8.6/10 (1,101 reviews)

During your visit to Rochester, you can do some window-shopping at Apache Mall. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Rochester Recreation Center

8.0/10 (205 reviews)

Catch an event at Rochester Recreation Center during your trip to Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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National Volleyball Center

7.8/10 (151 reviews)

Catch an event at National Volleyball Center during your trip to Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Welch Village Ski Area

8.6/10 (16 reviews)

Hit the slopes in Welch with a visit to Welch Village Ski Area. Stroll along the area's riverfront or simply enjoy its coffeehouses.

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Shattuck-St. Mary's School

9.6/10 (69 reviews)

Enjoy the collegiate vibe when you visit Shattuck-St. Mary's School, during your trip to Faribault. Visit the shops in this family-friendly area, or simply enjoy its coffeehouses.

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Mayowood Mansion

9.4/10 (29 reviews)

You can spend time browsing the exhibits at Mayowood Mansion in Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Learn more about Southeast Minnesota

Explore the family-friendly area of Southeast Minnesota—restaurants, sports teams, and sights from Mayowood Mansion to Apache Mall.

See all hotels in Southeast Minnesota

A lake surrounded by dense forest and a distant hill with a fort.

Top Southeast Minnesota Hotel Reviews

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"The room had some noise like water going thru some pipes during the early morning hours. Could be something due to the swimming pool. No sleep after that started."

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"Property and room was very clean. Shuttle was convenient for Mayo visit."

Express Suites Riverport Inn & Suites

8/10 Good

"Great breakfast. Beds a little firm. Thanks"

Hotel Indigo Rochester – Mayo Clinic Area by IHG

10/10 Excellent

"Staff was extremely helpful and knowledgeable. Restaurant was clean and food was great. Very close to everything and parking was easy and inexpensive."

Hyatt House Rochester/Mayo Clinic Area

10/10 Excellent

"B"

Brentwood Inn & Suites

8/10 Good

"While the property is old, I found it very clean. Location is excellent. Bed was not great. Staff was incredibly accommodating."

Kahler Inn and Suites - Mayo Clinic Area

10/10 Excellent

"The hotel was very nice and convenient for travel to the Mayo Clinic with direct access to the underground walk way. The room was clean and nice to have the continental breakfast option. Construction was taking place outside of the hotel to improve the Mayo Clinic buildings in the area. The windows seemed to be rather low on their sound proofing ability. Almost seemed like the windows were open at times."

The Plaza Hotel & Suites Winona

8/10 Good

"Wa"

Cobblestone Hotel & Suites - Austin

10/10 Excellent

"Clean, front desk was great."

More cheap stays in Southeast Minnesota

Super 8 by Wyndham Winona MN

1025 Sugar Loaf Rd Winona MN

CA $68

CA $77 total

Nov 15 - Nov 16

includes taxes & fees

Quality Inn near Medical Center

5708 Bandel Road NW Rochester MN

CA $88

CA $101 total

Nov 15 - Nov 16

includes taxes & fees

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $100

CA $115 total

Nov 24 - Nov 25

includes taxes & fees

7.8/10 Good! (1,033 reviews)

Best Western Rochester Hotel Mayo Clinic Area/St. Mary's

1517 16th St Sw Rochester MN

CA $139

CA $160 total

Nov 1 - Nov 2

includes taxes & fees

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $149

CA $165 total

Nov 1 - Nov 2

includes taxes & fees

8.8/10 Excellent! (835 reviews)

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $168

CA $193 total

Oct 29 - Oct 30

includes taxes & fees

8.8/10 Excellent! (1,005 reviews)

Hotels in Southeast Minnesota with star rating

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Rochester Vacations

Book Hotels in Southeast Minnesota on Expedia.com

Find hotels in Southeast Minnesota, MN from CA $77

Change your mind

Treat yourself

Be picky

Go beyond your typical stay in Southeast Minnesota

Check prices for these dates

Filter by

Star rating

Guest rating

Our top choices for Southeast Minnesota hotels

1. Hampton Inn & Suites Rochester-North

2. Comfort Inn & Suites Rochester South Mayo Clinic

3. Hotel Indigo Rochester – Mayo Clinic Area by IHG

4. EVEN Hotel Rochester - Mayo Clinic Area by IHG

5. Baymont by Wyndham Kasson Rochester Area

6. Spark by Hilton Rochester South

7. Sleep Inn & Suites West-Near Medical Center

8. Hyatt House Rochester/Mayo Clinic Area

9. Econo Lodge Mayo Clinic Area

10. Holiday Inn Express & Suites Rochester – Mayo Clinic Area by IHG

11. Home2 Suites by Hilton Rochester Mayo Clinic Area

12. AmericInn by Wyndham Rochester Near Mayo Clinic

13. Staybridge Suites Rochester - Mayo Clinic Area by IHG

14. Treasure Island Resort & Casino

15. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

16. Comfort Inn & Suites West - Medical Center

17. Quality Inn & Suites Mayo Clinic Area

18. Fairfield Inn & Suites Rochester Mayo Clinic Area/St. Marys

19. TownePlace Suites by Marriott Rochester

20. Holiday Inn Express Rochester South - Mayo Area by IHG

Vacation Rentals in Southeast Minnesota

The Berkman

Broadway Plaza, Trademark Collection by Wyndham

Lake Pepin Escape: Loft Cottage & Fireplace

1 Block to Lake City Marina: Condo w/ Rooftop Deck

Pet-friendly Wabasha Studio: Boat, Ski & Explore!

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

Stay near popular Southeast Minnesota attractions

Villa Bellezza

Mayo Civic Center

Apache Mall

Rochester Recreation Center

National Volleyball Center

Welch Village Ski Area

Shattuck-St. Mary's School

Mayowood Mansion

Learn more about Southeast Minnesota

Top Southeast Minnesota Hotel Reviews

AmericInn by Wyndham Rochester Near Mayo Clinic

EVEN Hotel Rochester - Mayo Clinic Area by IHG

Express Suites Riverport Inn & Suites

Hotel Indigo Rochester – Mayo Clinic Area by IHG

Hyatt House Rochester/Mayo Clinic Area

Brentwood Inn & Suites

Kahler Inn and Suites - Mayo Clinic Area

The Plaza Hotel & Suites Winona

Cobblestone Hotel & Suites - Austin

More cheap stays in Southeast Minnesota

Super 8 by Wyndham Winona MN

Quality Inn near Medical Center

Med City Inn & Suites - Mayo Clinic Area

Best Western Rochester Hotel Mayo Clinic Area/St. Mary's

Cobblestone Hotel & Suites - Austin

Brentwood Inn & Suites

Hotels in Southeast Minnesota with star rating

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