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

A mural of Red Wing with a steamship, houses, and a bridge.

Change your mind
Book hotels with free cancellation
Treat yourself
Sign in to save 10% or more on thousands of hotels
Sign in
Be picky
Search almost a million properties worldwide

Go beyond your typical stay in Southeast Minnesota

Pet friendly

Cabin

Spa

Hot tub

Villa

Pool

Apartment

Condo

Apart hotel

Cottage

Family friendly

Waterpark

Check prices for these dates

Tonight

Tomorrow

Next weekend

In two weeks

Our top choices for Southeast Minnesota hotels

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

A reception desk with a large digital screen displaying a cityscape and the word "happy."

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

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.

An indoor swimming pool with a checkered tile wall, a door labeled 'Mechanical Room,' and a window with a view outside.

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

2. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Terri

CA $105

CA $121 total

includes taxes & fees

Nov 7 - Nov 8

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

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

A modern interior with a wooden ceiling, a large black shelving unit, and a refrigerator stocked with beverages.

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

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

A reception area with a curved reception desk, wooden shelving, and a green moss wall with the text "I ♥ EVEN".

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

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 view through a sliding glass door to an outdoor area, a nightstand with a lamp, and a wooden headboard.

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

5. Baymont by Wyndham Kasson Rochester Area

Kasson

Dana

CA $92

CA $98 total

includes taxes & fees

Nov 1 - Nov 2

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

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

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

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

6. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

CA $108

CA $125 total

includes taxes & fees

Nov 22 - Nov 23

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

A small, well-organized pantry with shelves stocked with snacks and beverages.

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.

7. Spark by Hilton Rochester South

Rochester

Stanton

CA $94

CA $108 total

includes taxes & fees

Nov 1 - Nov 2

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

A modern bar area with seating and a counter.

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 indoor pool area with lounge chairs and a pool.

8. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Arlan

CA $178

CA $205 total

includes taxes & fees

Nov 13 - Nov 14

A hotel room with a large bed, a desk, a chair, a television, and a window with curtains.

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

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

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

9. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $93

CA $107 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 restaurant with a counter, seating area, and a TV screen.

An indoor swimming pool with wooden ceiling beams, yellow chairs, and tables along the sides.

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

11. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

CA $154

CA $177 total

includes taxes & fees

Nov 7 - Nov 8

A bar with wooden stools and a neon sign.

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

An indoor swimming pool with a slide, seating area, and a large frog statue.

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 urban street with tall buildings, a pedestrian walkway, and a parking area.

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

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

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

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

14. Comfort Inn & Suites West - Medical Center

Rochester

Tammy

CA $121

CA $139 total

includes taxes & fees

Nov 15 - Nov 16

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

A modern interior with a fireplace, a green armchair, and a patterned rug.

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

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

15. Treasure Island Resort & Casino

Welch

Kristine

CA $118

CA $147 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 modern reception area with a wooden reception desk, glass pendant lights, and a long hallway with seating.

A restaurant interior with wooden tables, chairs, and a stone wall.

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

16. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Deanna

CA $160

CA $184 total

includes taxes & fees

Oct 31 - Nov 1

A modern living room with a sofa, coffee table, and a TV mounted on a stone wall.

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

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

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

17. Quality Inn & Suites Mayo Clinic Area

Rochester

Jessica

CA $93

CA $109 total

includes taxes & fees

Nov 14 - Nov 15

An outdoor patio area with a concrete floor, wooden fence, and string lights.

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.

A Fairfield Inn & Suites hotel with a modern design, featuring a prominent entrance and a parking area.

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

A reception area with a wooden reception desk, a "Welcome to the Bread & Butter State" sign, and a "Please Center" sign.

A hotel room with a bed, a desk, a chair, a TV, and a bathroom visible through an open door.

A pool area with a table and chairs, a lifeguard chair, and a pool lift.

A modern lounge area with seating arrangements, a reception desk, and a patterned wall.

19. Hampton Inn Rochester-South

Rochester

dennis

CA $137

CA $158 total

includes taxes & fees

Nov 1 - Nov 2

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

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

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

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

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

Rochester

Rick

CA $115

CA $132 total

includes taxes & fees

Nov 7 - Nov 8

View all properties

Save an average of 15% on thousands of hotels when you're signed in

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.

See properties

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.

See properties

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.

See properties

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.

See properties

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.

See properties

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.

See properties

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.

See properties

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.

See properties

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

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."

AmericInn by Wyndham Rochester Near Mayo Clinic

10/10 Excellent

"nice breakfast"

Treasure Island Resort & Casino

10/10 Excellent

"Thank you"

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"

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 $133

CA $153 total

Oct 29 - Oct 30

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

Explore a world of travel with Expedia

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. Sleep Inn & Suites West-Near Medical Center

7. Spark by Hilton Rochester South

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. Comfort Inn & Suites West - Medical Center

15. Treasure Island Resort & Casino

16. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

17. Quality Inn & Suites Mayo Clinic Area

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

19. Hampton Inn Rochester-South

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

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

EVEN Hotel Rochester - Mayo Clinic Area by IHG

Express Suites Riverport Inn & Suites

Hotel Indigo Rochester – Mayo Clinic Area by IHG

AmericInn by Wyndham Rochester Near Mayo Clinic

Treasure Island Resort & Casino

Hyatt House Rochester/Mayo Clinic Area

Brentwood Inn & Suites

Kahler Inn and Suites - Mayo Clinic Area

The Plaza Hotel & Suites Winona

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

Explore a world of travel with Expedia

Go further with the Expedia app