•Heterotopic pancreas has rarely been identified in the wall of choledochal cysts.•Out of 200 surgically excised specimens of choledochal cysts, heterotopic pancreas was identified in 13 (6.5%) cases.•Sero-mucinous peribiliary glands were found intermingled with the heterotopic rests.•Inflammation and fibrosis are also noted within and around these rests.•Heterotopic rests and biliary tree may be of common embryogenic origin, and HP may be one of the causes of choledochal cyst formation. Heterotopic pancreas (HP) has rarely been identified in the wall of choledochal cyst (CC). Retrospectively we screened 200 excised specimens of CC received at our Institute over a period of last eight years and looked for presence of HP rests in them. All the specimens were processed in their entirety. HP was identified in the wall of 13 (6.5%) CCs, out of which 11 were Heinrich Type 2, and two were Heinrich Type 1. In half of the cases peribiliary mucous glands were observed intermingled with the HP rests. Features of chronic fibrosing pancreatitis were identified in these rests, with ulceration of overlying cyst lining. HP rests in the wall of CC though rare; their coexistence with peribiliary glands may possibly indicate their common embryonic origin. As a common site of inflammation, HP rest may be one of the common causes of CC.