Nanotechnology has been investigated for treatments of hair follicle disorders mainly because of the natural accumulation of solid nanoparticles in the follicular openings following a topical application, which provides a drug “targeting effect”. Despite the promising results regarding the therapeutic efficacy of topically applied nanoparticles, the literature has often presented controversial results regarding the targeting of hair follicle potential of nanoformulations. A closer look at the published works shows that study parameters such as the type of skin model, skin sections analyzed, employed controls, or even the extraction methodologies differ to a great extent among the studies, producing either unreliable results or precluding comparisons altogether. Hence, the present study proposes to review different skin models and methods for quantitative and qualitative analysis of follicular penetration of nano-entrapped drugs and their influence on the obtained results, as a way of providing more coherent study protocols for the intended application.