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Train from Linate to Varenna

We are flying into Linate airport, arriving at 6:00 pm. We would like to overnight near Linate in a mid-range hotel then take train to Varenna in the morning. Where can we stay and can we take a train without going to Milan central station?

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There is no train from Linate to Varenna that avoids Milan Centrale. In fact, you will most likely take a bus service from Linate to Milan Centrale. Linate is a lot closer to the Milan Centrale train station than Malpensa. From what I see in the RS book, there are two bus services. Starfly takes you from Linate to Milan Centrale. ATM (a bus line) takes you to a nearby metro stop where you then navigate the metro system to Milan Centrale. If you are traveling to Varenna by train, you will need to go through Milan Centrale.