Objective To analyze the effect of Noggin silencing on the BMP and Wnt signaling pathways in hair follicle development. Methods The expression of BMP-2, BMP-4, BMPR-IA, BMP-6, BMP-7, LEF-1 and β-catenin in Noggin silencing MC3T3-E1 stable cell line was detected by RT-PCR and western blot. Results RT-PCR results showed that the expressions of five genes in BMP signaling pathway were all significantly influenced by Noggin silencing, the expressions of BMP-2 (P<0.001), BMP-4 (P<0.01), BMP-6 (P<0.001) and BMP-7 (P<0.001) were all increased and the expression of BMPR-IA (P<0.01) was decreased. While the expressions of the two genes LEF-1 (P<0.001) and β-catenin (P<0.001) in Wnt signaling pathway were significantly decreased. Western blot results showed that the expressions of these proteins in the two signaling pathways were also affected. The expressions of BMP-2 (P<0.05), BMP-4 (P<0.05), BMP-6 (P<0.05) and BMP-7 (P<0.05) were all increased, while the expressions of BMPR-IA (P<0.05), LEF-1 (P<0.01) and β-catenin (P<0.001) were decreased. Conclusions There may be a negative feedback regulation of Noggin on the BMP signaling pathway in vitro, but a positive feedback regulation on the Wnt signaling pathway in vitro. It provides certain evidence for studies on the effect of Noggin gene on BMP and Wnt signaling pathways in vivo. There may be an interaction between hair follicle development-related signaling pathways, which still needs further experiments to prove.