Lipid-based Delivery Systems (LDS) has been the focus of potential strategies in drug delivery for several years. A great deal of work has been invested on how to exploit their biocompatible and biodegradable nature, in combination with their nanosize range in a profitable way in the field of nanomedicines. A number of drugs loaded in LDS have been already tested in vivo successfully. However, in vivo behaviour of nanosized materials differs from their bulk counterparts (and also change drug properties), mainly depending on the particular LDS physicochemical characteristics. These may have huge impact on the toxicity of the system, despite the physiological nature of the lipid materials. This note on the regulatory concerns and toxicity assessment in LDS suggests that current knowledge of public and scientific communities is lacking, requiring intensive research and policy measures to provide a deep understanding on toxicological risks.