Objective:To investigate the mechanism that small GTPase Arl6 regulates sonic hedgehog(Shh) signal transduction. Methods:The mRNA expression level of Gli1 and Ptch1,two Shh pathway target genes,were detected in Arl6 knockdown stable cell lines. The localization of Arl6 in the primary cilia was observed under confocal microscope. Ciliogenesis of Arl6 knockdown cells was quantified by counting the percentage of ciliated cells. Results:Knockdown of Arl6 inhibited full activation of the Shh pathway. After treatment with high-concentration Shh medium or Smo agonist Purm,Gli1 mRNA expression was significantly lower in the shArl6 group than in the control group (P < 0.01),and Ptch1 mRNA expression was also decreased (P < 0.05). Arl6 was located in the basal body of the primary cilia, and its absence resulted in defective ciliogenesis. Meanwhile,Shh signaling stimulated the expression of Arl6 (P < 0.05). Conclusion:Knockdown of small GTPase Arl6 inhibits full activation of Shh signaling,which is related to defective ciliogenesis.