A new measure of neuromuscular transmission instability, motor unit potential (MUP) jitter, is introduced. MUP jitter can be estimated quickly using MUP trains (MUPTs) extracted from electromyographic (EMG) signals acquired using conventional clinical equipment and needle EMG electrodiagnostic protocols. The primary motivation for developing MUP jitter is to avoid the technical demands associated with estimating jitter using conventional single fiber EMG techniques. At the core of the MUP jitter measure is a classifier capable of labeling a set of aligned MUP segments as single fiber MUP segments, i.e., parts of MUPs generated predominantly by a single fiber and not significantly contaminated by contributions from other fibers. For a set of MUPs generated by the same MU, these segments will have varying occurrence times within the MUPs, but will have consistent morphology across the MUPs. Pairs of sets of single fiber MUP segments generated by different fibers of the same MU and tracked across a MUPT can be used to estimate neuromuscular transmission instability. Aligning MUP segments is achieved using dynamic time warping. Results based on 680 simulated MUPTs show that MUP jitter can be estimated with an average error rate as low as 8.9%. Also, one or more sets of single fiber MUP segments can be detected in 85.3% of the studied trains. The analysis for a single MUPT can be completed in 3.6 s on average using a conventional personal computer.