The prevalence and incidence of basal cell carcinoma are on the rise. Yet, its histogenesis is still controversial. Hitherto discussed concepts are largely based on morphological analogies. Historically, basal cell carcinoma was named after its similarity to the epidermal basal cell layer which is viewed as its histogenetic origin. On the other hand, a primitive follicular origin is postulated due to the morphological similarity of basal cell carcinoma to the embryonic hair germ. In 1990, the hair follicle bulge was characterized as the anatomical niche for follicular stem cells. Early studies employing stem cell markers suggested a follicular origin of basal cell carcinoma. Since then an explosion of stem cell markers has occured in dermatology. In this review, the stem cell markers employed in the examination of basal cell carcinoma up to now are critically evaluated. Initially, studies on the histogenesis of this common dermatological tumor are reviewed.