In using eye movements to develop cognitive models, researchers typically analyze eye movement protocols with aggregate measures and test models with respect to these measures. Because aggregate analyses sometimes conceal informative low-level behavior, protocol analyses comparing model predictions to individual trial protocols are frequently desirable; however, protocol analysis for eye movement data is often tedious and time-consuming. We describe how to automate the protocol analysis of eye movements using hidden Markov models. Working with data from an equation-solving task, we demonstrate two methods of tracing eye movement data—that is, mapping eye movements to the sequential predictions of a cognitive process model. W e evaluated these tracing methods in an experiment where participants were instructed to execute given equation-solving strategies. When coding the experimental protocols in terms of the given strategies, the automated tracing methods performed as well as human expert coders in a fraction of the time.