The thyroid hormones have profound effects on the development of neuromuscular system. These hormones exert their influence on both muscle fibers and related motoneurons during development. Masseter is one of the most important muscles for mastication in mammals. Thyroid hormone deficiency 3 weeks after birth, the period in which an alteration from sucking to biting occurs, could influence the developmental pattern of the muscle. Horseradish peroxidase was injected into the masseter (0.5-5 µlit, 40%) of normal and prenatal hypothyroid pups at 1,7,15 and 23 postnatal days. After 24-48 h, the 50µm brainstem sections were processed for TMB histochemical procedure. Labeled motoneurons in Mo5 were counted, measured and on the basis of their tracing intensity classified into heavy (H), intermediate (I) and light (L) groups. In each age group motoneurons were divideded into small, intermediate and large populations. In 1-day old pups, there was no significant difference between the labeling intensity and size of motoneurons in normal and hypothyroid rats. From the day 7, a significant decrease in the number of H motoneurons was observed (P<0.05), I motoneurons remained unchanged,whereas the number of L motoneurons significantly increased in hypothyroid pups (P<0.05). A significant increase in the number of small motoneurons was observed in hypothyroid pups, medium sized neurons showed no change but large motoneurons significantly decreased in hypothyroid pups (P<0.05). These data suggest that at the end of sucking period (day 23), hypothyroid pups show a 6 days delay in their pattern of masseter innervation as compared to its normal development.