Does anyone know how long the train takes to travel from Rochester to Manhattan? (without delays!)
Thank you!

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For that you should look at Amtrak's schedule, but expect delays.
Its about 6 hours, I believe.
Just go to Amtrak.com, click Timetables, and select Empire Service. Travel time is about 7-8 hours.
You're probably there and back by now, but, just to share a rule of thumb, when you get tickets, be aware that train #48, in particular, comes from Chicago and is more likely to be quite late by the time it hits Rochester than the other trains are. On the other hand, #48 has a real Dining Car, while the other trains through Rochester have a snack car.