Objective The aim of this study was to observe the growth difference and expression of cytochrome C of skin hair follicles in neonatal mice. Methods The morphology of different skin hair follicles of neonatal mice(postnatal day 1-9)were observed by HE staining histology and cytochrome C was detected by immunohistochemistry. Results The skin hair follicles in different parts of neonatal mice showed differences not only in morphology but also in developmental periods. Hair follicle growth in the back and tail skin had a nonlinear and growing period. After the nonlinear and growing period they began to grow rapidly. The tail development was slightly slower than that on the back. The hair follicles of vibrissae were very special, and started to develop without a stable period. Conclusions The results of morphological observation and cytochrome C immunohistochemistry demonstrate that differences exist in the hair follicle morphology and developmental times in the skin of different parts of the body in neonatal mice.