Atypical condyloma is a variant of flat condyloma characterized by the presence of atypical koilocytes having large hyperchromatic, smudged and often bizarre nuclei. Atypical condyloma can be frequently misdiagnosed on cytologic smear and on tissue sections by its marked cellular atypia, as high grade dysplasia, in situ or even invasive squamous cell carcinoma. We described two cases of atypical condyloma of the female genital tract. The cytologic features and histologic changes were reminiscent of those of invasive squamous cell carcinoma and severe degree of dysplasia of the uterine cervix. The differential findings between atypical condyloma and squamous cell carcinoma were discussed in detail.