The distribution and axonal transport of cholinergic organelles has been studied in the rat motor system, using immunofluorescence methods and a cytofluorimetric technique for quantification of immunoreactive material. Crush-operated spinal roots and sympathectomized sciatic nerves were sectioned longitudinally and incubated with antisera against p38, SV2, CGRP, chromogranin A (Chr A), synapsin I (SYN I), and with RASVA (rabbit anti-synaptic vesicle antiserum). Motor endplates were also studied. It was observed that proximally accumulating organelles--i.e., organelles which were in transport distally in the axons--contained RASVA-like immunoreactivity (LI) p38, SV2, CGRP-LI, Chr A-LI, and SYN I-LI. Retrogradely transported organelles, however, contained only p38 and SV2 in addition to RASVA-LI, but virtually no CGRP-LI, ChrA-LI, or SYN I-LI. It is suggested that the rapid axonal transport mechanism operates in the nerves like a chromatographic process, which allows the concentration in the axons, proximal or distal to the crush, of organelles in anterograde or retrograde transport, respectively. The technique of nerve crushes in combination with immunocytochemistry can therefore be used to investigate the biochemical composition of organelles in transit along the axon, and give information on neurobiological events occurring in these long processes leading to the nerve endings. In this study, biochemical differences between anterogradely and retrogradely transported cholinergic organelles in the motor neuron of the rat have been observed, and were related to suggested events in the endplate.