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Arriving by public transportation (scheduled services):
-- from Milan's Malpensa airport - there are two options:
1. via Como and Bellagio -- train from airport to Como Lago Nord (changing at Saronno), then proceed by #C30 bus to Bellagio. From Bellagio, take one of the frequent ferries across the lake to Varenna. Alternatively, it is possible to take a (less frequent) direct boat service from Como to Varenna (info on same website, the boat's final destination is usually Colico).
2. via Milan -- train or bus from airport to Milan's central train station, then train to Varenna. Trains are listed on the station boards showing their final destination, i.e., either Sondrio or Tirano. Exit the train at Varenna-Esino.
Option 1 is much more scenic, as part of the trip is on or along the lake, but ferries and buses do not run very late in the evenings, especially in the off-season.
-- from Milan's Linate airport -- bus to Milan's central train station, then train as above.
-- from Milan/Bergamo airport -- bus to Bergamo train station , then train (website as above). Service is every hour, but there always is a train change in Lecco.
-- from central Milan - take a train from central station as indicated above.
-- from any other location within the Lombardia region - plan your trip using the regional government website
-- from Venice: there are two possible routes by train:
1. via Milan - one train change only, in Milan. Route is longer, though, and relatively more expensive as most trains on the Venice/Milan route are now EuroStar City trains. Refer to the Trenitalia website linked above for timetable information.
2. via Bergamo - two changes, typically in Brescia and Lecco, but shorter (and cheaper) route.
Arriving by car:
The SS36 is a dual carriageway, toll-free highway that runs all along the eastern shore of Lake Como. There is a well signposted exit for Varenna. Alternatively, use the older coastal road (very narrow and winding, but probably more scenic, as the highway runs inland and has lots of long tunnels).
Once in town, there is parking between the train station and the ferry pier, as well as along the stretch of road leaving town toward Fiumelatte, and in the newly constructed parking garage on the opposite side of the street.