Hey guys,
we're in the process of planning our Tibet trip (last two weeks of April) and this forum has been very supportive. One issue we have right now is that our preferred tour company is unable to arrange for a train ticket from Shanghai to Lhasa. I have read all the information on sites like seat61.com but I'm looking for any recent experience in getting such a ticket without going through one of the agencies (which seem to charge a high fee). Has anyone done this by themselves?

Problems you are going to have getting the train tickets yourself include:
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Probably needing at least the copy of the Tibet permit in order to buy the tickets.
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Probably you don't get the Tibet permit until quite close to the departure date.
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By that time, all the hard and soft sleeper tickets have sold out.
If the flights are available at a discount, I'd fly.
Drumbrake is spot on....unless you are able to get at least a copy of your Tibet Travel Permit by the time tickets go on sale (which is normally 10 days in advance going to Lhasa), you are probably going to have a hard time getting the tickets on your own. In general, Shanghai and Guangzhou are the mot difficult places to take the train to Lhasa from as it is not a common place for foreigners to begin their journey to Tibet from. Xining is the best option as it is the official starting point of the Tibetan Railway and because most agencies can easily get train tickets to Lhasa from there.