Damage diagnosis based on a bank of Kalman filters, each one conditioned on a specific hypothesized system condition, is a well recognized and powerful diagnostic tool. This multi-hypothesis approach can be applied to a wide range of damage conditions. In this paper, we will focus on the diagnosis of cracks in rotating machinery. The question we address is: how to optimize the multi-hypothesis algorithm with respect to the uncertainty of the spatial form and location of cracks and their resulting dynamic effects. First, we formulate a measure of the reliability of the diagnostic algorithm, and then we discuss modifications of the diagnostic algorithm for the maximization of the reliability. The reliability of a diagnostic algorithm is measured by the amount of uncertainty consistent with no-failure of the diagnosis. Uncertainty is quantitatively represented with convex models.