Eigenproblem has wide range of applications in engineering disciplines, including compression and recognition. When building practical systems for these applications, we are interested in actual system performance. The actual system performance usually differs from the ideal system performance. One way to quantify the actual performance is to measure the ideal performance and the performance degradation/perturbation. In this paper, we present a system performance perturbation analysis particular to eigen-systems based on matrix perturbation theory. Such performance analysis can provide guidance for designing practically good systems.