Background It is important for surgical purposes to know the biliary tract anatomy and its variations in detail. The aim of the study was to evaluate the frequency of anatomical variations of the biliary tract at hepatic bifurcation level and also at cystic duct level using magnetic resonance cholangiopancreatography (MRCP). Methods A total of 1041 patients (between 16 and 102 years of age, 600 women 441 men with mean age of 60.6) were included in the study. The MRCP imaging was carried out with a 1.5 Tesla magnetic resonance imaging (MRI) device by using heavily T2-weighted sequences. Results Among the 1041 patients included in the study, 424 (40.7 %) showed anatomical variations at different levels of the biliary tree, and 12 of these patients (1.15 %) had two anatomical variations. Typical anatomy was present in 57.2 % of the females and 62.1 % males. The highest incidence of variation at the level of bifurcation was trifurcation with 133 patients (12.8 %) and at the level of cystic duct was the medial cystic duct insertion with 56 patients (5.37 %). Conclusions Trifurcation and medial cystic duct insertion seem to be more frequent in females compared to males. It is necessary to have the knowledge of these variations to avoid possible complications and also help to achieve the most effective result. MRCP