Couple of questions:
1) So i'm trying to figure out what the difference is between italiarail and trenitalia.
2) What should I take to go from Rome to Florence if I want to stop by Pisa for an afternoon on the way?
3) Which routes do you recommend (or trains) to go from:
Naples to Rome,
Rome to Florence (with stop at Pisa)
Florence to Venice
Any help would be greatly appreciated thank you!
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I think Italiarail is just a reseller. Trenitalia is the official train operator
You can check Trenitalia to see if makes sense to go from Rome to Pisa and then Florence or to Pisa from Florence on a different day
http://www.trenitalia.com/cms/v/index.jsp?vgnextoid=ad1ce14114bc9110VgnVCM10000080a3e90aRCRD
ps. How long will you be there altogether (not counting flying in and out days)?
>>What should I take to go from Rome to Florence if I want to stop by Pisa for an afternoon on the way?<<
You would take a high speed train from "Roma Termini" to "Pisa Centrale".
After sightseeing in Pisa, take one of the frequent regional trains from "Pisa Centrale" to "Firenze S. M. Novella" for Florence.
Many of the best train options between Rome and Pisa will pass through Florence, thus vjpblovesitaly's suggestion that it might be more efficient to do Pisa as a half-day trip from Florence.
I woud suggest travel straight to Florence from Rome. There is a day bus tour that starts from outside Florence train station. Not just Pisa you would also visit beautiful tuscany towns of sienna, San Giginiminano and wine producing farm for a lunch. All for $100 is worth the trip.
There are two competing train operating companies on Italy's main railway trunk routes: Italotreno (privately owned) and Trenitalia (the public brand of the state railway holding company). They use the same track, but different stations, in Milan and Rome.
This means timings can be different, and their prices move independently of each other. I THINK most tourists (but absolutely not most Romans) would find the station Italotreno uses in Rome a bit out of the way, though that depends where you're staying. But you need to check both companies' offerings on your route on your day.
The two companies' rolling stock on fast trains (Italotreno has no others) on your proposed routes is broadly similar. Both make a bit of a fuss on their websites about their premium classes - but for a 90 min journey, what's the point?
Italotreno doesn't serve Pisa: most people would go Rome-Florence, then make a sidetrip to Pisa.
>>>2) What should I take to go from Rome to Florence if I want to stop by Pisa for an afternoon on the way?<<<
Pisa is not on the way to Florence (check a map).
Take the fast AV trains between Naples/Rome (70 minutes), Rome/Florence (85 minutes), Florence/Venice (2 hours). You can book all these on Trenitalia 120 days in advance. You'll often find discounted tickets as cheap as 9€-19€.
For Pisa, visit from Florence by train (7€ one way). Do not buy these tickets online as there are more restrictions. Buy in Florence and remember to validate these before you board (your fast train tickets don't need validating - they will be checked on board).
If you decide to take the train that goes up the coast in order to visit Pisa (it takes 3-4 hours!) on the way to Florence, you will need to check your luggage at the station in Pisa (Centrale). Some of these trains are the faster AV trains (3 hours) and the others are the slower regional trains (4 hours).