Background: Genital warts are a common infectious sexually transmitted disease. Autophagy plays an essential role in eliminating pathogenic viruses and it is regulated by autophagy-related genes (ATGs). Beclin-1 gene is known to be one of ATGs, mediates autophagosome formation. Many viruses have evolved strategies to interfere with the formation or maturation of autophagosomes. There are lack of studies evaluating serum and tissue expression of Beclin-1 gene in genital HPV (human papilloma virus) infections and their correlation with the disease outcome. Aim: To measure tissue expression of Beclin-1gene and its protein level in plasma in patients with genital warts. Patients and Methods: This cross-sectional study was conducted at Dermatology Outpatient Clinic and Andrology, Infertility and Sexually Transmitted Diseases Outpatient Clinic of the Suez Canal University Hospitals, Ismailia. The study included two groups; 30 patients with genital wart and 30 healthy controls. Beclin-1 gene expression in plasma and in tissue biopsies of 30 patients with genital warts was measured using real time polymerase chain reaction (PCR) and Beclin-1 protein level in plasma of both groups was measured using enzyme-linked immunosorbent assay (ELISA). Results: Both Beclin-1 gene expression in plasma and Beclin-1 protein level in plasma and their tissue expression were significantly decreased in genital warts patients compared to controls. Conclusion: Beclin-1 as an essential ATG with its critical role in the formation of autophagosome, which may affect cellular defense and immune response to pathogens, provides a promising therapeutic target for new treatment modalities of infectious diseases.