Hi @jac08 We usually stay at the Marriott Residence Inn on Center Street, which is connected via the subway (underground walkway) to the clinic. They’re pet friendly and also located in an area with plenty of sidewalks and pet friendly trails for exercise.
Many of the hotels have kitchenettes or full kitchens which feels more like home for food prep and storage.

These sites might also be helpful for you.
~bringfido.com
https://www.bringfido.com/lodging/city/rochester_mn_us/
~petswelcome.com
https://www.petswelcome.com/pet-friendly-hotels/minnesota/rochester
When you decide on a hotel, there can be an advantage to calling directly to that hotel to get the best rate. Most of the hotels near the clinic will offer a Mayo patient discount.
Do you have a dog or kitty?