Aim: To compare the frequency of infections with the bacteria Chlamydia trachomatis and Neisseria gonorrhoeae in different biological samples in men during the period from January 1, 2022 to December 31, 2022 in the Department of Immunological and Molecular Diagnostics of the Clinic for Infectious Diseases "Dr. Fran Mihaljević". Methods: From the laboratory data base of the Department of Immunology and Molecular Diagnostics of the Clinic for Infectious Diseases "Dr. Fran Mihaljević" patient data and results were retrospectively collected and analyzed using the statistical package Statistica 13.3 (available at https://statistica.software.informer.com/). Data on the gender and age of the patients, type of biological sample and results of DNA testing of bacteria C. trachomatis and N. gonorrhoeae were collected. DNA detection of bacteria C. trachomatis and N. gonorrhoeae at the Clinic for Infectious Diseases "Dr. Fran Mihaljević" is performed on the Abbott m2000 system using the Abbott RealTime CT/NG test on urine samples, oropharyngeal swabs and rectal swabs. Results: Three types of biological samples (urine, oropharyngeal swab and rectal swab) were analyzed for the presenceof DNA bacteria Chlamydia trachomatis and Neisseria gonorrhoeae in 372 patients who received clinical care in the Outpatient Clinic for Sexually Transmitted Diseases in Men of the Institute for Infections of Immunocompromised Patients. 250 (67.2%) patientswere negative for both bacteria, 27 (7.2%) were positive for both bacteria, 36 (9.8%) patients were positive only for C. trachomatis and 55 (14, 7%) of patients were positive only for N. gonorrhoeae. PCR reaction inhibition was detected in only 4 (1.07%) patients, all of which were rectal swab samples. Most of the tested patients wer ebetween 20 and 32 years old. Conclusions: The results of this retrospective study indicate the importance of molecular testing in sexually transmitted infections, especially in screening and asymptomatic patients. Today, molecular methods for the detection of sexually transmitted infections are becoming 48 the standard due to their high sensitivity and rapid detection of bacteria. Rectal and oropharyngeal swab samples are increasingly being used for screening because most of such infections are asymptomatic, and in the future patients will be able to collect samples themselves, which will reduce the clinical burden. The short coming of this research is insufficient information about the patients' anamnesis. In future research, data from the patients' anamnesis should be taken into account, so it would be possible to learn more about the symptoms of infections themselves, the frequency of asymptomatic positive infections and the connection of this type of sexual infections with other sexually transmitted diseases.