Though a number of backpackers travel independently all over Afghanistan every year, there is only one area of the country that is really safe for tourists: the Wakhan Valley and Afghan Pamir, accessible from Tajikistan, are the only areas that the Taliban never occupied and have not seen any fighting or terrorism. It is also one of the country’s most isolated areas, with some villages and yurt encampments a 7 day walk from the nearest road, electricity or shop. Amid the stark 7000m+ scenery, yak and donkey caravans ply a 1-month on foot trade route from Badakshan in the West to The Little Pamir in the East. Snow leopards, bears and Marco Polo sheep can be spotted.
The Wakhan can be accessed from Tajikistan without ever having to enter less stable parts of Afghanistan. First you will need to go to the Tajik town of Khorog, either by 24 hour shared car from the Tajik capital of Dushanbe (several depart every day) or by flight. At the Afghan consulate in Khorog they issue 1-month Afghan tourist visas on the spot for US$50 with no need for an invitation, accommodation booking or guided tour. However, remember that if you want to exit Afghanistan back into Tajikistan, without having to visit less stable parts of Afghanistan, you will need a double-entry Tajik visa.
From Khorog you will need to go to the Tajik town of Ishkashim, 2-3 hours away, Go to the part of the Khorog bazaar where shared taxis wait and cross the footbridge over the river. This is where shared taxis to Ishkashim go from. Just outside the Tajik town of Ishkashim there is a footbridge across the river to the Afghan town of Ishkashim.
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