Experimental evidence points to the importance of mitochondrial transport defects in contributing to major neurodegenerative diseases, such as Parkinson’s disease (PD). Studies of mitochondrial transport along single axons are difficult with traditional dissociated culture systems and the fragility of the midbrain dopaminergic cultures precludes their survival in previously developed microfluidic devices with an enclosed architecture. Using soft lithography, we generated a microdevice from polydimethylsiloxane (PDMS) for the purpose of studying the transport of mitochondria along single dopaminergic axons. The device comprises two large open culture chambers connected by a parallel array of microchannels that achieves fluidic separation of axons from the soma and allows the tracking of mitochondrial movement along oriented axons. Dopaminergic neurons from midbrain cultures were successfully cultured within the microdevices for up to 4 weeks and extended their axons across the microchannels. Axonal mitochondria within the microchannels were labeled by transduction with a mitochondrial-targeted DsRed2 lentiviral vector or with the mitochondria-specific dye, Mitotracker Deep Red and were visually tracked with conventional confocal microscopy. The methodology and device that we have described here will allow further study of the role of mitochondrial transport defects play in major neurodegenerative diseases.