Heparin is an anticoagulant which administrated usually either by Intravenous or Subcutaneous injection. This study aimed to formulate microemulsions containing heparin using nonionic surfactants for transdermal application. Five microemulsions were developed and characterized for their rheological properties and droplets size. The in vitro permeation of heparin was measured using Franz diffusion cell. Hence, an HPLC-method was developed to study the permeability through the skin. Furthermore the efficacy of one developed heparin was orally and transdermally tested using rats model in comparison to subcutaneous administration. The rheograms and droplets size measurements evidenced that the developed drug delivery systems are microemulsions. Furthermore, the permeation of heparin using MEs could be proved using Franz diffusion cells. Moreover, the in vivo results could reflect the effect of absorbed heparin through the skin as well as after oral administration. Finally the novel MEs containing heparin can be promised carriers for noninvasive application of heparin.