(1) Background: Sexually Transmitted Infections (STIs) in men are a significant public health problem due to the consequences they can have, such as chronic diseases, infertility, cancer, and even death. This study aimed to determine the frequency of microorganisms associated with STIs in men with urethritis attending urology consultations, and to explore their clinical correlations. (2) Methods: A population that attended the urology consultation of the University Hospital “Dr. José E. González” was studied. Written consent was obtained, and interviews and clinical history were conducted about specific risk factors identifying signs and symptoms associated with any genitourinary condition; after that, urine samples were collected. Identification of C. trachomatis, N. gonorrhoeae, U. urealyticum, and M. genitalium was based on amplifying species-specific DNA fragments. (3) Results: A total of 200 patients were included. The mean age was 55 years (20–95). According to the interviews, only 32.5% (n = 65) had received prior sex education. Additionally, 75% (n = 150) do not usually use any protection during sexual intercourse. Regarding clinical factors, 69.4% (n = 138) presented burning or pain when urinating. Molecular analysis revealed the presence of C. trachomatis to be 9.5% (n = 19), with U. urealyticum at 13% (n = 26), and M. genitalium at 2% (n = 4). (4) Conclusions: This is the most extensive molecular epidemiological study of the frequency of STIs in men in Mexico in third-level care and its association with different risk factors. As reported globally, a similar frequency of C. trachomatis, U. urealyticum, and M. genitalium was detected.