Crimp and bulk, important wool fiber properties, are thought to be related to differences in the protein composition of the orthocortex and paracortex. Fiber morphological studies have demonstrated that the paracortex has a higher proportion of matrix and cysteine than the orthocortex. While there is some evidence for the differential expression of genes between these cell types in the follicle, this has not been demonstrated satisfactorily in the mature fiber. Using proteolytic digestion of wool fibers, followed by ultrasonic disruption to obtain relatively pure fractions of both cell types, the KAP3 high sulfur protein family was found to be present in higher concentrations in the paracortex. This significant finding provides an explanation for the higher cysteine content reported in the paracortex. This represents an advance in our understanding of protein expression variation in the orthocortex and paracortex, and how this relates to key physical and mechanical properties of wool fibers.