Appropriate functionality of nodes of Ranvier, presynaptic terminals, and other axonal subdomains depends on efficient and timely delivery of proteins synthesized and packaged into membrane-bound organelles (MBOs) within the neuronal cell body. MBOs are transported and delivered to their final sites of utilization within axons by a cellular process known as fast axonal transport (FAT). Conventional kinesin, the most abundant multisubunit motor protein expressed in mature neurons, is responsible for FAT of a large variety of MBOs and plays a major role in the maintenance of appropriate axonal connectivity. Consistent with the variety and large number of discrete subdomains within axons, experimental evidence revealed the identity of several protein kinases that modulate specific functional activities of conventional kinesin. Thus, methods for the analysis of kinase activity and conventional kinesin phosphorylation facilitate the study of FAT regulation in health and disease conditions. Axonal degeneration, abnormal patterns of protein phosphorylation, and deficits in FAT represent early pathological features characteristic of neurological diseases caused by unrelated neuropathogenic proteins. Interestingly, some of these proteins were shown to produce deficits in FAT by modulating the activity of specific protein kinases involved in conventional kinesin phosphorylation. However, experimental systems that facilitate an evaluation of molecular events within axons remain scarce. Using the isolated squid axoplasm preparation, we describe methods for evaluating axon-autonomous effects of neuropathogenic proteins on the activity of protein kinases. Protocols are also provided to evaluate the effect of such proteins on the phosphorylation of endogenous axonal substrates, including conventional kinesin and neurofilaments.