Horseradish peroxidase conjugates of either the lectin wheat germ agglutinin (WGA-HRP) or choleragenoid (B-HRP) have been shown to be sensitive neuroanatomical tracers. In the present study a comparison was made between these two conjugates as transganglionic tracers in trigeminal primary sensory neurons following injection into the rat mystacial vibrissae skin. Differences between the two tracers were observed in the labeling of cell bodies in the trigeminal ganglion. Injection of WGA-HRP resulted in labeling of predominantly small cell bodies, whereas B-HRP gave rise to labeling of somewhat larger cell bodies. By increasing the concentration of the injected WGA-HRP solution the number of labeled cells increased substantially, while a corresponding increase in the concentration of B-HRP resulted in a relatively small increase in the number of labeled cells. WGA-HRP injection resulted in labeling of primary afferents mainly in the substantia gelatinosa of the trigeminal subnucleus caudalis. When the concentration of the injected WGA-HRP solution was increased, labeling was also observed in the marginal and magnocellular zones. Following B-HRP injection, labeling was only observed in the magnocellular zone and innermost part of the substantia gelatinosa. This general pattern of labeling was the same when the concentration of the B-HRP solution was increased.