© 2016, Springer Science+Business Media New York. We estimate the success probability of quantum protocols composed of Clifford operations in the presence of Pauli errors. Our method is derived from the fault-point formalism previously used to determine the success rate of low-distance error correction codes. Here we apply it to a wider range of quantum protocols and identify circuit structures that allow for efficient calculation of the exact success probability and even the final distribution of output states. As examples, we apply our method to the Bernstein–Vazirani algorithm and the Steane [[7,1,3]] quantum error correction code and compare the results to Monte Carlo simulations.