Toxicity of nanoparticles is a current scientific issue because of the enhanced reactivity of nanomaterials and their possible easy penetration into the body arising from their small size. Because inorganic particles are present in sunscreen cosmetic products, attention has been focused on cutaneous penetration. But organic particles of various sizes are also used in pharmaceutical applications such as skin care and transdermal drug delivery. It appears that organic and inorganic particles penetrate the skin quite differently. The apparent discrepancy is addressed in this review focusing on skin penetration of inorganic sunscreen particles and organic particles for drug delivery. After a short description of the physicochemical properties of these particles, the skin penetration of both types is reviewed with emphasis on the mechanistic issues and the differences that could account for such conflicting results. It appears that investigations by cosmetic and pharmaceutical communities focused on the main issue, i.e., no toxicity in cosmetics and maximum activity of the drug in pharmaceutics. This leaves several fundamental issues as open questions and this does not allow a rigorous comparison between both types of material. While it is claimed that inorganic nanoparticles can only penetrate the outer layer of the skin, it appears that organic submicron particles and even microparticles reach the dermis in an in vitro cell. Besides particle size, the surface chemistry of the particles and the presence of other excipients in the formulations contribute to skin absorption.