Background HOXA9 (Homeobox A9), whose expression is promoted by MLL1 (Mixed Lineage Leukemia 1) and WDR5 (WD-40 repeat protein 5), is a homeodomain-containing transcription factor which plays an essential role in regulating stem cell activity. HOXA9 inhibits regeneration of skeletal muscle and delays the recovery after muscle wound in aged mice, but is little known in denervated/reinnervated muscles. Methods we performed detailed time-process expression analysis on HOXA9 and its promotors, MLL1 and WDR5, in the rat gastrocnemius muscle after three types of sciatic nerve surgeries: nerve transection (denervation); end-to-end repairing (repairing); and the sham operation. Then the specific mechanisms of Hoxa9 were detected in vitro through primary satellite cells transfected respectively by pIRES2-DsRed2 empty plasmids, pIRES2-DsRed2-HOXA9 plasmids, pPLK/ GFP -Puro empty plasmids, and pPLK/GFP-Puro- HOXA9 shRNA plasmids. Results We found that HOXA9 expression was synchronous with the severity of muscle atrophy, as well as the upregulation of MLL1 and WDR5 associated with the denervation state to some extent. Indeed, experiments with primary satellite cells revealed that HOXA9 inhibited myogenic differentiation, but not destroy the differentiation potential, influenced the best-known atrophic pathways, and promoted apoptosis. Conclusion HOXA9 may play a pro-atrophic role in denervated muscle atrophy.