Purity of deinterleaved pulse descriptor word (PDW) trains is critical to the performance of emitter classification software that analyzes PDW data. Contamination of the input PDW train can lead to artifacts in the analysis resulting in incorrect or ambiguous classification. This paper presents results of an investigation into the possibility of applying transition matrices to the detection and removal of contaminating pulses from a deinterleaver output. The utility of transition matrices as a fast and efficient pattern recognition tool in ESM emitter classification has been known for over a decade [Brown, R.G., "Pattern Recognition Using Transition Matrices", 7th RMC Symposium on Applications of Advanced Software in Engineering, pp 52-57, Royal Military College of Canada, Kingston Ontario, May 1995]. In the work presented herein, transition matrix patterns unique to contaminated pulse trains are sought in order to provide a warning that a particular PDW train is contaminated, and provide a clue as to which pulses should be removed to purify the PDW train.