Infections caused by Neisseria gonorrhoeae and Chlamydia trachomatis are one of the most significant healthcare issues worldwide. When studying the medical history data, it is necessary to consider the features of the sexual behavior of patients. Extragenital forms of N. gonorrhoeae (pharyngeal, rectal) are detected in 5—15% of patients, most commonly in men who have sex with men (MSM). Extragenital forms of C. trachomatis are well studied in men, in addition, rectal form of C. trachomatis is the most frequent in MSM. However, these forms can be found in women. The extragenital (rectal and pharyngeal) forms of Neisseria gonorrhoeae and Chlamydia trachomatis are often asymptomatic, which can complicate their diagnosis and treatment. There are differences in the choice of treatment strategies for genital and extragenital forms of sexually transmitted infections, furthermore, non-optimal treatment can lead to the spread of resistant microorganisms. In this article we analyzed modern approaches to the therapy of genital and extragenital forms of N. gonorrhoeae and C. trachomatis in Russia and foreign countries with emphasis on differences in guidelines, efficacy of treatment regimens and problems of antimicrobial resistance.