Highlights iPSC-derived dopaminergic neurons from LRRK2 patients show extensive endocytic changes. Integrated proteomic and transcriptomic approach reveals dysregulation of 25 RABs. Functional impairment of clathrin mediated endocytosis in LRRK2 iPSC-dopaminergic neurons. Aged LRRK2 rats also show similar perturbations of key endocytic proteins. LRRK2 human post-mortem tissue shows upregulation of clathrin and endophilin.