Motivated by recent applications of pushdown systems to computer security problems, we present an efficient algorithm for the reachability problem of alternating pushdown systems. Although the algorithm is exponential, a careful analysis reveals that the exponent is usually small in typical applications. We show that the algorithm can be used to compute winning regions in pushdown games. In a second contribution, we observe that the algorithm runs in polynomial time for a certain subproblem, and show that the computation of certificate chains with threshold certificates in the SPKI/SDSI authorization framework can be reduced to this subproblem. We present a detailed complexity analysis of the algorithm and its application, and report on experimental results obtained with a prototype implementation.