Jefferson Lines
(http://www.jeffersonlines.com) offers service to many cities, plus connects to Greyhound in Minneapolis. Jefferson Lines buses stop at the Sinclair gas station located at 205 6th St SW. If part of your trip involves travel on Greyhound (http://www.greyhound.com), you can purchase your ticket on Greyhound's website, which will cover travel on both carriers.
By plane
Rochester International Airport
IATA: RST (http://www.rochesterintla...) is 10 miles south of downtown Rochester along Hwy 63. Due to the large number of visitors to the Mayo Clinic, there are more flights than in comparably-sized cities, approximately 15-20 per day. Delta Air Lines (http://www.delta.com/)) has flights from Minneapolis/St. Paul and Detroit. American Airlines (http://www.aa.com/) offers direct service from Chicago O'Hare. Allegiant Air (http://www.allegiantair.com/) is going to offer direct flights to Phoenix starting November 1st, 2012. Allegiant used to offer twice-weekly flights from Las Vegas but that ended on 2/15/2010. However, the airline is considering bringing the flights back.The airport attempting to get more air service into Rochester. The airport directors have recently contacted the current providers, American and Delta, about adding more destinations, and have also contacted United, Frontier, and Allegiant to bring new nonstop destinations to the airport.
There are several car-rental companies located at the airport. Taxis are relatively expensive, approximately $25 between downtown Rochester and the airport. Shuttle service is available, timed to meet each arrival; one-way fare to downtown hotels is approximately $11.50. Some hotels also provide shuttle service. Make sure you fly into Rochester, MN, not Rochester, NY!
Minneapolis-Saint Paul International Airport
IATA: MSP (http://www.mspairport.com) is a 90-min drive NW of Rochester. A major airport, it has flights from most major cities around the world. Dominated by Delta Air Lines. Go Rochester Direct (http://www.gorochesterdir...) and Rochester Shuttle Service (http://rochestershuttlese...) offer scheduled shuttle service between MSP and Rochester. Star Limousine Service (http://www.limostar.com/a...) and Gold Crown Limo (http://www.goldcrownlimo.com/) offer private sedan service.When flying in to Rochester, it is worth checking flights into both airports. Flights in to and out of Rochester are typically slightly more expensive about $50; however, as with all things related to airfares, this varies widely.
By train
There is no train service into Rochester. The closest station is 45 minutes drive away in Winona. However, ground transportation between Rochester and Winona is available from GoCarefree Shuttle (http://www.gocarefreeshut...). However, GoCarefree Shuttle does not wait in Winona for passengers disembarking at the Winona Amtrak station seeking transit to Rochester.
By car
The closest interstate to Rochester is I-90 running east and west across Minnesota. There are two exits from I-90 that will take you north into Rochester, US Highway 63 when coming from the west and US Highway 52 Exit 218 when coming from the east.
US Highway 14 runs east and west through Rochester, connecting Rochester with Winona and Owatonna. Highway 14 east is a 4-lane freeway in Rochester with the exception of a partial cloverleaf.
US Highway 63 runs north and south through Rochester and is the main north-south thoroughfare through downtown Rochester, and connects Rochester with Lake City and south to Waterloo and connect you up with the Avenue of the Saints. It is a 4-lane expressway between I-90 and US 52, with a freeway portion in the last couple of miles towards Highway 52.
US Highway 52 also runs north and south through Rochester and is the main pipeline connecting Rochester with the Twin Cities and running south to the southeast corner of Minnesota and into Iowa. It is a 6-lane freeway.