NATO has continually ignored Russian objections to the U.S. led plans for a missile defense shield in Europe. Now the Russians have threatened that they may no longer allow NATO to use Russian territory to transport supplies to the NATO mission in Afghanistan.
Although the northern supply route is more expensive than through Pakistan the route through Russia has been more secure. Pakistan has for now shut off transport routes in protest against NATO killing 24 of its troops. The Pakistan route is often attacked by militants even when it is functioning.
NATO has dismissed the Russian complaints continually. Russia has now also said that it may set up its own ballistic missiles on the borders of the EU. Russia believes that the missile shield is deployed against Russia rather than Iran which according to NATO is the primary grounds for the shield. For more see this article.