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Is it reasonably possible to currently travel from Juba to Khartoum (or vice versa) over land? How? What would be the route? What would be the transport?

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Considering recent border conflicts I would suggest you check travel advice from your government on this issue. My guess is that it would be best to leave it for a year or two. South Sudan is a new nation in the process of building up its government offices. For one border stations might not be properly set up. I guess getting a VISA on the border might be difficult. Taking vehicles across borders could in itself be a challenge.

Roads are of course subject to general quality and seasonal changes. A shallow search on the net indicates that the rainy season may make it near impossible to travel the stretch.

In a discussion on the Lonely Planet webpages back in 2008 someone asked the same question as you:

Basically - it sounds like a bad idea. But one of the contributors in the above hiked from the south to the north. Quite recently it seems. The person also mentions that parts of the trip might be done by boat from Malakal to Juba.

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Thanks. Though that's a lot of (educated) guesses. As far as I know, there are currently no real border conflicts, there are few, if any, usable roads and it is definitely not possible to officially get a visa at the border. The boat trip is not scheduled and might or might not exist. You see, all these 'maybes' and the most recent online info being years old is why I asked the question :) –  MastaBaba Nov 21 '12 at 6:08
    
Agree. It's a fair amount of guesswork. Still I think the link I dug up to discussions on Lonely planet site could be useful. –  ragnvald Nov 21 '12 at 6:44
    
There are a few more threads on the thorn tree, but none are really recent (say, post-independence). –  MastaBaba Nov 21 '12 at 10:16
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