Investigations concerning the penetration of topically applied drugs are the subject of a multiplicity of research, as the exact knowledge of these mechanisms is the prerequisite for the optimization of such substances. As the hair follicles represent a good long-term reservoir for topically applied substances, it can be assumed that they also represent a reservoir for microorganisms residing on and in the skin. Therefore, the hair follicles must be seen as one main site of action for antimicrobial substances and a simple non-invasive in vivo method for the determination of penetration of antimicrobial substances into the hair follicles. The aim of the present study was to show that differential stripping, by removing the hair follicle content selectively, represents a suitable method to demonstrate the penetration of antifungal substances into the hair follicles. The follicular casts, removed from skin areas of human volunteers, which were partially pre-treated with brilliant green (well-known antifungal properties), were applied on agar plates inoculated with Candida albicans. The results showed inhibited growth of C. albicans, if the follicular casts were removed from skin areas pre-treated with brilliant green. This indicates clear evidence that brilliant green had penetrated into the hair follicles. Therefore, differential stripping represents a suitable method to determine the penetration of antifungal substances into the hair follicles, which is of clinical importance for the optimization of topical antifungal therapeutics.