Dopaminergic neuron cell death in Parkinson’s Disease (PD) is complex and combinatorial, with impairments in multiple cellular pathways impacting mitochondrial function, endosomal/lysosomal protein degradation, alpha-synuclein and tau aggregation, and neuroinflammation. Genetic risk factors, such as mutations in leucine-rich repeat kinase 2 (LRRK2) and glucocerebrosidase (GBA), have been shown to impact kinetics of the autophagiclysosomal pathway (ALP), which is suggested to contribute to PD-associated protein accumulation and aggregation. Human-relevant in vitro models using patient-derived induced pluripotent stem cells (iPSCs) offer an accessible avenue for understanding the mechanisms for these genetic mutations as well for development of therapeutics against this debilitating disease. In this study, we evaluated the expression and cellular distribution of ALP-associated proteins in iPSC-derived dopaminergic neurons (iCell® DopaNeurons) generated from both apparently healthy normal donors (AHN) and patients clinically diagnosed with Parkinson’s Disease and harboring a LRRK2 G2019S mutation. Disease iPSCs were obtained from the Parkinson’s Progression Markers Initiative (PPMI), part of The Michael J. Fox Foundation (MJFF). Using high-throughput imaging we quantified mitochondrial and lysosomal protein expression using an array of highly specific antibodies from Cell Signaling Technology (CST), including LAMP-1, LC3, Cathepsin B, and CoxIV. Together, these data demonstrate the utility of high-throughput immunocytochemistry and patient-derived iPSC dopaminergic neurons for investigating lysosomal, mitochondrial, neurodegenerative pathway dynamics.