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Getting a visa to South Sudan is an easy task - just keep in mind that the Government of Southern Sudan´s Yellow Travel Permit does NOT allow for travel to North Sudan. In fact, the Government of National Unity (north) might delay a visa request to the north if a traveller first obtained a GoSS Travel Permit.
To get a GoSS Yellow Travel Permit - take the Yellow Fever Vaccine and get a Certificate.
Visit the nearest GoSS Liaison Office, submit an application (together with 2 passport photos, Yellow Fever Vaccination Certificate, Letter of Invite, and some USD - normally around 50 USD), then pick up your Travel Permit the next day. Easiest is through the Nairobi-, Kampala- or Addis- based GoSS Liaison Offices.
Get the same GoSS Travel Permit if you are planning to cross the border by land (Uganda and Kenyan borders) - and prepare to be patient at the border crossing if you´re arriving by bus.
Note: 9th July 2011 South Sudan becomes Independent - visa/GoSS Travel Permit rules might change.
Getting a Sudanese visa can be a random experience, depending on where you apply, what day of the week it is, and the phase of the moon. Currently the most reliable place to get a visa is in Cairo, where they are issued same-day for $100.
Addis Ababa can be a difficult place to get a visa, it is usually quicker to fly to Cairo and get a visa rather than wait for one in Addis Ababa. However it can be random, people have been occasionally known to get a visa in a couple of days in Addis.
You must have no evidence of having visited Israel in your passport. This includes exit stamps from border posts in countries bordering Israel. A recently issued passport by your embassy with no stamps is suspicious to the Sudanese that you are trying to hide evidence of having visited Israel.
Crossing the Border
This information applies to crossing overland from Egypt to Sudan.
The only open border is by taking the weekly ferry from Aswan in Egypt to Wadi Halfa in Sudan. There may appear to be on the map other border crossings but the land border is most definitely closed to tourists.
Go and see the very helpful Mr Salah at the Nile Navigation Company in Aswan. If you have a vehicle, it will cost you approximately EP 2500 for the vehicle and EP 383 per passenger in First Class, EP 250 in second class. First class you get your own stinky cabin, second class you get deck space (maybe, if you get on board early enough). It's cheaper for a motorbike.
The vehicle will not go on the ferry, it will go on a barge that goes separately from the ferry and arrives in Wadi Halfa a couple of days after the ferry (depending on the weather and whether the barge breaks down!). If you have a large vehicle (over 5m long) you may have to charter your own barge (again from the Nile Navigation Co) as your vehicle will not fit widthways on the standard barge. You will have to negotiate a price for this - have heard of people getting the barge for EP 17,000, and you can fit up to 5 vehicles on the barge.
Once you get to Wadi Halfa, the port is a couple of km from the 'town' (such as it is). Once you have got through immigration and customs (straightforward and hassle free - you did get your visa in Cairo for U.S.$100 in 24 hours didn't you?!), you will be greeted by a bunch of guys trying to get you to take their beaten up old land rovers into Wadi Halfa town. They will take advantage of your green-ness and try and charge you 500 sudanese dinars(about U.S.$2) per person (10 to a Land Rover) for this 2km trip. The right price should be about 50 sudanese dinars, but they are unlikely to take that. There is further confusion because youare not sure whether they are quoting sudanese pounds or sudanese dinars (there are 10 pounds to the dinar). Anyway, it's not that bad, follow the railway line to walk into town. You might even get a free lift from a minibus..
In Wadi Halfa itself there are an equally dismal selection of 'hotels', all with long-drop toilets and bucket showers. The standard price is 700 dinars per bed (4 beds to a room) and no amount of haggling will reduce this. You can change dollars to dinars at the bank in Wadi Halfa at a non-rip-off rate. You need to register with the police which is expensive at U.S.$33 each (payable either in dollars or dinars, compare the prices as one is slightly more than the other).
Your transport will arrive a day or two later. To get your vehicle off the barge and out of customs without costing you a fortune can be a challenge. It helps if there is a big group of you and you stick together and nobody goes off opening their wallet to get the job done quicker. This is something for which you need LOTS of patience. Have heard stories of people paying U.S.$500 for the ramps to get their vehicle off the barge, do not do this, just sit and wait and eventually they will cave in, they have to get the barge back to Aswan for the next load...
The total fees for clearing the vehicle through customs should come to around 5,100 dinars. This consists of customs duties of 1,600 dinar (make sure they stamp your Carnet), port taxes of 2,000 to 2,900 dinar depending on the size of the car, and a local tax of 1,000 dinar.
You may be asked to give a contribution/baksheesh to the guy filling out the arabic customs paperwork for you, 1,000 dinar per vehicle (U.S.$4) is the most you should pay. If you are asked to pay U.S.$20 per vehicle, as has been known to happen, just refuse and sit there... eventually it will get to 6pm and they will want to close up the customs shed and they will let you go - you might even got away without paying the local tax they were so keen to get rid of you. It helps if you have a bunch of you and you all stick together.
This information is current as of February 2006. [note as of January 2007 the dinar has been replaced with the (new) Sudanese Pound at a rate of 100 dinar to the (new) pound]