Introduction and objective: One of the main precursory lesions for pancreatic carcinoma is pancreatic cystic neoplasm. Differentiation between the various types of cysts is a clinical challenge. The microbiome colonizing the pancreatic cyst fluid is mostly unknown. The aim of the study was microbiological assessment of pancreatic cysts compared with biochemical parameters and histopathological results. Material and methods: 30 patients with pancreatic cysts undergoing surgery in 2022-2023 at the Department of General and Transplant Surgery, Medical University of Lodz, were enrolled in the study. Preoperative biochemical levels of blood parameters were analysed. Bacterial culture results were taken from the nasal vestibule, the skin of the groin, as well as from cyst fluid and bile (in case of cholecystectomy) and histopathological reports were analysed. Results: Mean age was 58.77±13.56 years. 10 patients (33.3%) had malignant lesions. Nine patients (30%) had positive cultures from cyst fluid. 6 of them had malignant conditions. Enterobacter cloacae, Enterococcus faecium Staphylococcus spp. were found. In the malignant group, patients were statistically significantly older (68.40±5.70 y vs. 53.95±13.86 y, p=0.004), tumour diameters were smaller (4.00±2.00 cm vs. 8.50±5.77 cm, p=0.003) and CA 19-9 level were higher (100.22±186.46 ng/ml vs. 12.35±16.08 ng/ml, p=0.045) than in a benign group. Conclusions: The occurrence of specific types of bacteria in patients with malignant pancreatic cysts appears to be of significant clinical importance. Further studies are needed.