Huntingtin (htt) is a ubiquitous scaffolding protein that regulates intracellular transport by linking motor proteins to organelles. Huntingtin-mediated bidirectional transport by kinesins and dynein in neural axons is essential to transcription, nucleocytoplasmic shuttling, synaptic function, and apoptosis. Polyglutamine expansion (PolyQ) in HTT causes Huntingtin's Disease (HD), a fatal neurodegenerative disease characterized by a gradual loss of motor control and cognitive ability. Increasing polyglutamine repeat lengths lead to earlier onset and greater severity of neurodegeneration. Defects in intracellular transport have been observed in cellular and animal models expressing PolyQ mutant huntingtin (mhtt). We aim to elucidate the effect of mhtt on interactions between motor proteins, vesicular cargoes, and cytoskeletal components in the transport complex to further understand it's role in neurodegenerative processes. We employ gene-edited, isogenic HD (isoHD) human embryonic stem cell (hESC) lines with 18Q, 30Q, 45Q and 81Q repeats in the first exon of HTT in our explorations to characterize transport under native conditions (18Q and 30Q), and to identify mHTT-related discrepancies associated late (45Q) and severe, early (81Q) onset of HD. We developed methods to isolate BDNF-containing organelles from ESC-derived neurons, reconstitute their motility along microtubules in vitro, visualize their motility using high-resolution imaging techniques and quantify the motors and adaptors bound to them. We first asked if BDNF organelles are trafficked along the signalling or degradative pathway. We find that BDNF-containing cargos co-localize with lysosomes 60-90 minutes post-internalization. Additionally, frequent co-localization of these cargos with lysosomes occurs earlier post-internalization in the 18Q lines than in the 45Q or 81Q lines, indicating that HD mutations might delay fusion with lysosomes. Our investigations will answer the questions of 1) which regulatory mechanisms involving htt govern intracellular transport and 2) how mhtt misregulates these processes.