The process of instrumenting a program to study its behavior can lead to perturbations in the program's execution. These perturbations can become severe for large parallel systems or problem sizes, even when one captures only high level events. In this paper, we address the important issue of eliminating execution perturbations caused by high-level instrumentation of SPMD programs. We will describe perturbation analysis techniques for common computation and com­munication measurements, and show examples which demonstrate the effectiveness of these techniques in practice.