Motor unit number estimation (MUNE) allows for quantitative assessment of functional motor units in a nerve. Several techniques have been applied to human studies. Although MUNE has been performed in animals to study neurological disorders, reproducibility has not been addressed. We analyzed the test-retest reproducibility of an incremental MUNE technique in rabbits and performed histological correlation. A peroneal MUNE was performed in 9 rabbits on two occasions separated by 30 days. MUNE was then performed on 18 rabbits prior to euthanize. A count of total fibers and a second count of large myelinated fibers were performed on nerve cross-sections. Test-retest reproducibility revealed an intraclass correlation coefficient (ICC) of 0.75. The average test-retest relative difference was 26.6%. Comparison of MUNE and histomorphometrical counts revealed a correlation coefficient (r) of 0.21 (total fiber counts) and 0.27 (large fibers). Although incremental MUNE has a high degree of reproducibility in rabbits, there is poor correlation with histological fiber counts.