The automatic coding of clinical documents is an important task for today's healthcare providers. Though it can be viewed as multi-label document classification, the coding problem has the interesting property that most code assignments can be supported by a single phrase found in the input document. We propose a Lexically-Triggered Hidden Markov Model (LT-HMM) that leverages these phrases to improve coding accuracy. The LT-HMM works in two stages: first, a lexical match is performed against a term dictionary to collect a set of candidate codes for a document. Next, a discriminative HMM selects the best subset of codes to assign to the document by tagging candidates as present or absent. By confirming codes proposed by a dictionary, the LT-HMM can share features across codes, enabling strong performance even on rare codes. In fact, we are able to recover codes that do not occur in the training set at all. Our approach achieves the best ever performance on the 2007 Medical NLP Challenge test set, with an F-measure of 89.84.