Background and Objective: The aim of this study was to detect bacteria associated with biliary tract diseases and relationship between their class 1, 2 and 3 integrons and antibiotic resistance patterns. Materials and Methods: Bile samples of biliary patients undergoing cholangiopancreatography were examined for the presence of bacteria and antibiotic resistance patterns using biochemical tests and disk diffusion method. PCR was used for detection of the presence of integrase genes intI1, intI2, and intI3 in total DNA and plasmid extracts of these bacterial isolates. Results: Out of 102 bile samples, 41.2% were positive by culture. The isolated bacteria belonged to E. coli (35.5%), Enterococcus spp. (19.4%), Klebsiella pneumoniae (17.74%), Pseudomonas aeruginosa (17.74%), Acinetobacter spp. (6.45%) and Staphylococcus epidermidis (1.6%). All isolates were resistant to amoxiclav and 87.5% of the isolates showed multidrug resistance (MDR) pattern. intI1and intI2 were found in E. coli (59.09%, 50%), P. aeruginosa (81.81%, 45.45%), K. pneumonia (63.6%, 27.27%) and Acinetobacter spp. (100%, 100 %), respectively. These results showed the presence of class 1 and 2 integrons on the extracted plasmids and indicated a significant association between class 1 integron and resistance to gentamicin and ciprofloxacin. Conclusion: High frequency of class 1 and 2 integrons among the bile isolates and their association with increased antimicrobial resistance phenotypes suggests that bile components are as selective agents for bacterial strains encoding these elements.