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Background: Human papillomavirus (HPV) infected keratinocyte dysfunction results in the formation of genital warts, and the specific role of Sonic hedgehog (SHh) signaling in genital warts remains elusive. Thus, this study aimed to identify the correlation between wart formation and SHh signaling. Materials and methods: In this study, nine male patients with genital warts were recruited, and the expression of SHh and its downstream signal molecules Patched‐1 and GLI family zinc finger 1 (Ptch1 and Gli1) was detected. Moreover, G2‐phase cells in the collected genital warts samples were assessed with normal foreskin samples as a comparison. HPV6/11 were detected via in situ hybridization (ISH), and SHh expression of the corresponding paraffin sections was determined via immunohistochemical staining (IHC). In addition, an in vitro down‐regulated SHh model was constructed by siRNA transfection of the HaCaT cell line, and the cell cycle was detected at 36 h by flow cytometry with propidium iodide staining. Results: SHh, Ptch1, and Gli1 in warts were significantly downregulated in the condyloma acuminatum (CA) group compared to the normal foreskin group. G2‐phase cells in the middle section of the spinous layer of CA wart tissues were significantly increased. Moreover, the expression of HPV‐DNA was amplified and negatively correlated with SHh activity in CA wart tissues. Lastly, the downregulation of SHh‐induced G2 arrest in vitro. Conclusions: The downregulation of the SHh signaling promotes HPV replication and the formation of warts by inducing G2/M arrest in the keratinocytes of CA. [ABSTRACT FROM AUTHOR]