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Trains from Livorno

We will be on a cruise and will be in Livorno, Italy, arriving on Wed, May 9, at 8am, and departing on Thurs May 10 at 6pm. We want to travel by train on our own rather than take cruise-sponsored tours. We would like to see Cinque Terra on one day and Siena on another, but are concerned with train schedules/reliability/available time at destination, plus connections to/from cruise ship and train station. What itineraries would you suggest and what trains would be recommended: time/class/destination?
If our Thursday schedule/destinations look too tight, what alternative destinations for Thursday would you suggest besides Pisa.

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There are several trains departing Livorno Centrale (name used on Trenitalia) to the CT. The firs train after you arrive on 5/9 departs at 9:17am and arrives in Riomaggiore at 11:18am. One train change at La Spezia Centrale for about an hour. Bummer. You can take later trains for a shorter journey but they will arrive after noon. You can actually buy the tickets right now (I see a mini-fare on 5/9 for the high-speed from Livorno Centrale to La Spezia Centrale (9E). This will help you avoid the long lines at the train station with the other cruise passengers. Also, your seat will be reserved. I suggested Riomaggiore as its a great starting point to walk the famous Via dell'Amore trail to Manarola. It takes about 30 minutes and is quite level. It's paved most of the way. Very scenic. Or, you can take the train to other towns first. There are several trains in the afternoon that will return you to Livorno Centrale. For the journey from Livorno Centrale, I see three trains departing at 7:30, 8:12 and 9:06. One train change at Empoli. Both of these trains are Regionale trains and you cannot buy online until you are within 7 days of travel. The R/T fare is 19.20E. No seat reservations permitted on the Regionales. Thus, its like a bus. You get on and if there are no seats, you stand. It's OK. A seat will open up a passengers get off. The important part is the return. The last two trains to make it back on time depart Siena at 12:41 and 13:41. They arrive at Livorno Centrale at 14:50 and 15:50 respectively. That gives you an hour to get from the train station to the ship by 5:00pm. Note that the Siena train station is almost a mile slightly downhill. from the city. Both journeys are 2+ hours out and 2+ hours to return to Livorno.