Abstract Purpose: To compare the effectiveness of anal and perianal condylomata treatment using argon plasma and electrofulguration. Methods: From January 2013 to April 2014, 37 patients with anal and perianal condylomata, who had been diagnosed through proctological examination, oncotic cytology, polymerase chain reaction (PCR) and histology, underwent treatment with argon plasma and electrofulguration. The perianal and anal regions were divided into two semicircles. Each semicircle was treated using one of the methods by means of simple randomization. Therapeutic sessions were repeated until all clinical signs of infection by HPV were eliminated. The patients were evaluated according to several variables like the genotype of HPV, HIV infection, oncological potential per genotype, oncotic cytology and histology. Results: Among all the variables studied, only immunosuppression due to HIV influenced the results, specifically when the fulguration method was used. There was no significant difference in effectiveness between argon and fulguration based on lesion relapse (p > 0.05). However, among HIV-positive patients, fulguration presented worse results, with a significant difference (p = 0.01). Conclusion: Regarding treatment of anal and perianal condylomata acuminata, comparison between applying fulguration and argon demonstrated that these methods were equivalent, but use of fulguration presented more relapses among HIV-positive patients.