During the Soviet War in Afghanistan, why did the refugee surge into Iran not have a destabilizing effect like it did in Pakistan?

Simple answer. Iran is an authoritarian government, a theocracy that is run by a bunch of mullahs. As such, they could (and possibly did) quash any dissent by mobilizing the Revolutionary Guards.

For all we know, Iran may have forcibly kept the refugees out.

Pakistan is somewhat freer than Iran, and not a theocracy, and is a government, that at least to a degree, believes in a democracy and open society of some sort.

If/when no one here has much of an idea, I would try asking this sort of question on http://history.stackexchange.com/ .

From research on-line, up to 2.5 million Afghans live in Iran, with up to 1 million being officially refugees. The UN states that about half of these refugees were ethnic Hazaras, who are a Shia minority in Afghanistan. It appears as if those fleeing to Iran were primarily trying to escape Sunni and Socialist religious persecution. Those who fled to Pakistan were also seeking to escape Socialist religious persecution and Sunni extremism. However, those who fled Afghanistan with radical religious agendas chose Pakistan, as these people were primarily Sunnis, and Pakistan is predominantly Sunni.

It is surprising that Iran did not chose to arm some of these Shiite refugees during the Afghan Soviet War. At the time they were tied down in their war with Iraq. Perhaps they thought it was not a good idea to pick a fight with the Soviet Union. I would not be surprised if many Afghan Shias, and other Afghans, chose to stay in Iran simply because they found it more stable than Afghanistan (or Pakistan).

Brian Ghilliotti