The high surface-to-volume ratio of polymeric nanofibers makes them an effective vehicle for the release of bioactive molecules and compounds such as growth factors, drugs, herbal extracts and gene sequences. Synthetic polymers are commonly used as sensors, reinforcements and energy storage, whereas natural polymers are more prone to mimicking an extracellular matrix. Natural polymers are a renewable resource and classified as an environmentally friendly material, which might be used in different techniques to produce nanofibers for biomedical applications such as tissue engineering, implantable medical devices, antimicrobial barriers and wound dressings, among others. This review sheds some light on the advantages of natural over synthetic polymeric materials for nanofiber production. Also, the most important techniques employed to produce natural nanofibers are presented. Moreover, some pieces of evidence regarding toxicology and cell-interactions using natural nanofibers are discussed. Clearly, the potential extrapolation of such laboratory results into human health application should be addressed cautiously.