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Our top choices for Southeast Minnesota hotels

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

1. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Arlan

HK$1,066 total

includes taxes & fees

27 Nov - 28 Nov

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

2. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

James

HK$1,136 total

includes taxes & fees

6 Nov - 7 Nov

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

3. Hampton Inn & Suites Rochester-North

Rochester

Mark

HK$913 total

includes taxes & fees

7 Nov - 8 Nov

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

4. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

HK$990 total

includes taxes & fees

7 Nov - 8 Nov

A modern living room with a flat-screen TV, a fireplace, a sofa, a coffee table, and a view of a cityscape through large windows.

5. Hilton Rochester Mayo Clinic Area

Downtown Rochester

Jennifer

HK$1,528 total

includes taxes & fees

27 Nov - 28 Nov

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

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

Kutzky Park

Brien

HK$1,049 total

includes taxes & fees

7 Nov - 8 Nov

A coffee shop interior with a wooden counter, menu boards, and seating area.

7. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Cory

HK$1,237 total

includes taxes & fees

7 Nov - 8 Nov

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

8. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

Naomi

HK$840 total

includes taxes & fees

28 Nov - 29 Nov

An outdoor patio with a brick floor, stone fireplace, and wooden pergola.

9. Homewood Suites by Hilton Rochester Mayo Clinic Area / Saint Marys

Kutzky Park

Lin

HK$990 total

includes taxes & fees

25 Nov - 26 Nov

A modern living room with a fireplace, comfortable seating, and large windows.

10. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Amanda

HK$1,045 total

includes taxes & fees

29 Nov - 30 Nov

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

11. Comfort Inn & Suites West - Medical Center

Rochester

Tammy

HK$785 total

includes taxes & fees

6 Nov - 7 Nov

A Comfort Inn & Suites hotel with a modern design, featuring a prominent signage and a parking lot.

12. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Terri

HK$645 total

includes taxes & fees

28 Nov - 29 Nov

A modern hotel lobby with multiple seating areas, including a central dining table with chairs, a bar area, and a seating section with cushioned chairs.

13. SpringHill Suites by Marriott Rochester-Mayo Clinic/St Marys

Kutzky Park

Jackie

HK$1,008 total

includes taxes & fees

22 Nov - 23 Nov

A room with a fireplace, two leather armchairs, a sofa, and a large window providing a view of the outdoors.

14. Brentwood Inn & Suites

Downtown Rochester

Elaine

HK$1,084 total

includes taxes & fees

2 Nov - 3 Nov

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

15. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Deanna

HK$1,031 total

includes taxes & fees

1 Nov - 2 Nov

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

16. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

HK$720 total

includes taxes & fees

7 Nov - 8 Nov

A swimming pool with clear blue water, surrounded by lounge chairs and a view of residential buildings through large windows.

17. Residence Inn by Marriott Rochester Mayo Clinic Area South

Rochester

Chee

HK$1,192 total

includes taxes & fees

27 Nov - 28 Nov

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

18. Hampton Inn Rochester-South

Rochester

Susan

HK$883 total

includes taxes & fees

15 Nov - 16 Nov

A swimming pool with a glass ceiling, a neon sign for the KAFFLER HOTEL, and a view of the city skyline at dusk.

19. Kahler Grand Hotel

Downtown Rochester

Carla

HK$1,278 total

includes taxes & fees

26 Nov - 27 Nov

A Staybridge Suites hotel with a stone facade, a covered entrance, and multiple windows.

20. Staybridge Suites Rochester - Commerce Dr NW by IHG

Rochester

MATTHEW

HK$1,048 total

includes taxes & fees

7 Nov - 8 Nov

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Holiday Rentals in Southeast Minnesota

Aparthotel

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

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.

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.

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.

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.

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.

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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Learn more about Southeast Minnesota

Discover the family-friendly area of Southeast Minnesota—sports teams, a scenic riverfront 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

"We’ve been to this property numerous times over the past 2 years for appointments in Rochester and have been pleased. Price has been decent as well."

Cobblestone Hotel & Suites - Austin

10/10 Excellent

"We’ve stayed here before while traveling through and decided to stay again. Pleasant staff, quiet rooms, comfortable bed and pillows, large and plentiful towels (my pet peeve is stingy and cheap towels). Breakfast was very nice with good options including bacon. Rates are quite reasonable. We’ll be back."