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We present an ammonia sensor for human breath analysis based on electrically conducting polymer nanojunctions. Each nanojunction is formed by bridging a pair of gold nanoelectrodes on a silicon chip separated by a small gap (<60 nm) with electrodeposited polyaniline. The signal transduction mechanism of the sensor is the change in the nanojunction conductance as a result of polymer dedoping by ammonia. The sensor response to human breath is validated by comparison with a reference method for detection of ammonium ion combined with an optimized breath ammonia trapping system. The nanojunction sensor is capable of in situ detection of parts per billion (ppb) levels of ammonia in human breath.