Objective To investigate the expression of inducible nitric oxide synthase (iNOS) and hypoxia inducible factor-1α(HIF-1α) and their effect on development of condyloma acuminatum (CA). Methods A total of 50 patients with CA and 20 healthy volunteers were collected. The expression of iNOS, HIF-1α and CD34 was determined by Immunohistochemistry. Results A total of 50 cases with CA were identified as iNOS positive (100%) which were expressed in whole epidermis; 14 out of 20 volunteers (70%) were iNOS positive (weak signal) which were mainly expressed in epidermal basal cells. Gray value of iNOS in CA patients was higher than that in healthy volunteers (97.9854 ±20.3196 vs 73.0174 ±15.6330, respectively) (p < 0.05). Fortytwo out of 50 patients (84%) experienced increased expression of HIF-1α while only 9 volunteers had positive signals (45%) (p < 0.05). Gray value of HIF-1α in CA patients was higher than that in the control group (0.2035 ±0.0637 vs 0.1349 ±0.0194) (p < 0.05). Intimate correlation between iNOS or HIF-1α and CD34 in CA was observed ( r= 0.375 and 0.393,p < 0.05). Conclusion iNOS and HIF-1α is involved in the pathogenesis of CA.