Background: Nabothian cysts are common benign cervical lesions often discovered incidentally during routine gynecological examinations. While they are typically asymptomatic, they may occasionally present with various clinical complaints. This study aimed to correlate between cytological or bacteriological findings and presence of nabothian cysts. Methods: This prospective observational study was carried out on one hundred women with confirmed cervical Nabothian cysts. The study was conducted at the Obstetrics and Gynecology Department of Benha University Hospitals between April 2022 and December 2022. Detailed clinical evaluations, including history taking, transvaginal ultrasound examination, cytological diagnosis using the Papanicolaou method, and bacteriological examination of cervical swabs and cyst aspirates, were performed. Results were analyzed to assess the characteristics of Nabothian cysts, cytological findings, and microbiological assessments. Results: Of the 100 participants, 60% were in the 31-40 age range, with 37% having two children. Complaints included 63% reporting discharge, 51% experiencing pelvic pain, and 8% facing infertility issues. Most cysts (68%) were larger than 10mm and located in the upper part of the cervix (57%). Cytological results revealed 8% with intraepithelial lesions and 3% with malignancy. Bacteriological assessments showed 40% had bacterial growth, with 28% displaying gram-negative bacilli. The presence of bacterial growth correlated with inflammatory changes and malignancy. Conclusion: Cytological and bacteriological assessments of Nabothian cysts in women with related complaints can provide valuable insights into their etiology and associated conditions. The presence of bacterial growth and specific bacterial strains may be linked to inflammatory changes and malignancy in these cysts.