The Background: Antimicrobial peptides are first line of defense for mucosa against viruses, bacteria, protozoa and fungi. Meanwhile, expression of antimicrobial peptides in postpartum period has not been studied. Objective: To estimate the expression of mRNA of antimicrobial peptides in epithelium of the cervix uteri after caesarean section and vaginal birth 3 or 4 days after delivery. Materials and methods: The data-sample consisted of 17 women after caesarean section and 46 women after vaginal delivery examined on days 3 or 4 of postpartum period. Quantitative reverse transcription PCR method was used to study mRNA expression of antimicrobial peptides. Statistical analysis was performed using Mann-Whitney criteria. Results: It was shown that higher level of expression of SLPI, HNP3, HD6 and HBD4 in the endocervix was present in women who delivered via caesarean section compared with those who had vaginal delivery. Conclusion: Women who underwent caesarean section exhibited increased expression of antimicrobial peptides compared to those who had vaginal birth. This increased expression can be attributed to multiple reasons such as differences in vaginal microflora restoration, different changes in hormone levels and also due to surgical trauma after operative delivery. The use of antimicrobial peptides can give new opportunities for prophylaxis and treatment of septic complications that occur in postpartum period.