Abstract Objective To evaluate the role of genital pathogens in postoperative morbidity following diathermy loop excision of the transformation zone (LETZ) of the uterine cervix. Methods Patients with cervical intraepithelial neoplasia (CIN) who underwent diathermy LETZ were included in a prospective study. Cervical swabs for genital pathogens were collected before the diathermy procedure. After surgery, women were followed-up regarding the occurrence and severity of postoperative pain, bleeding, and discharge. Results Genital pathogens were present in 463 of 788 (58.8%) cases. The most frequently isolated groups of microorganisms were group B β-hemolytic Streptococcus , α-hemolytic Streptococcus , Enterococcus species, and coliforms. In patients with genital pathogens, postoperative pain was present in 298 (37.8%), discharge in 262 (33.2%), and bleeding in 236 (29.9%) cases. In patients without genital pathogens, 199 (25.3%) experienced pain, 181 (23.0%) discharge, and 143 (18.1%) bleeding. The differences between the 2 groups were not statistically significant ( χ2 for pain = 0.675; χ2 for discharge = 0.031; χ2 for bleeding = 3.444; P > 0.05). Conclusion Genital pathogens are very common among patients with CIN and do not affect the occurrence or severity of pain, discharge, or postoperative bleeding after diathermy LETZ.