This summer I would like to fly into Rome, Italy and sightsee for three days, then take a train to Venice. After staying in Venice for one day and night, I would like to take a day train through the eastern Alps to Salzburg or Innsbruk. After two days there, then take a train to Munich. Visit Munich area for three days and then fly back to US. Can this trip be done in 10 -12 days (two of those days would be flight days)? Are there day trains that travel through Italy and the Eastern Alps? Can anyone suggest an agenda?
From Rome to Munich via Salzburg
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You can use www.bahn.com to look at nearly all possible train connections on your own. The summer schedules are not all out yet, but the same day of the week in January gives you a good idea of what is possible and how frequently they run. The schedule does not change that much between the seasons. Italy has a second company, Italo train, connecting major cities. But they run roughly parallel to what you already see at www.bahn.com, so no new info for the route planning purpose.
To sum up: you have 8-10 days to visit Rome, Venice, Innsbruck or Salzburg and Munich plus the train travel between the cities - I think, it's possible.
There is a Eurocity connecting Munich, Innsbruck, Bozen and Verona every two hours, 5:30 h, nice train.
Salzburg is 1h from each, Innsbruck and Munich.
Coming from Venice, you usually have to change trains in Verona (trains from venice usually continue to the west/Milano).
What do you expect Innsbruck and Salzburg to be like?
When you expect "a city surrounded by mountains", I'd also consider visiting Bozen. For architecture, maybe also Verona instead of Salzburg. But that's maybe a matter of taste.
Also, for short glimpses, you could hop on and off the Eurocity in Verona, Bozen and Innsbruck.
If I had to choose between SALZBURG or INNSBRUCK I would do SALZBURG. There is just not that much to see in Innsbruck and we have been through there numerous times over the years. We enjoyed the Belvedere Hotel on our last trip in Salzburg in 2007.
Spend time in VENICE. A very interesing city as is MUNICH.