Purpose of the present work was to study in vitro permeation of gold nanoparticles (NPs) through isolated rat skin and intestine. Another objective was to see the effect of particle size on permeation of the gold NP. Gold NP of 15 nm, 102 nm and 198 nm were synthesized and used for study. Franz diffusion cells were used to evaluate permeation of gold NP from rat skin whereas 'intestinal sac' method was used for assessing intestinal permeation. Number density of gold NP was analyzed by UV-vis spectroscopy whereas amount of gold permeated was measured by ICP mass spectrometry. The absorption and localization of gold NP through rat skin was studied by TEM. Qualitative analysis of gold inside of the rat skin was performed by energy dispersive X-ray spectroscopy (EDS). Gold NP showed negative zeta potential. UV-vis absorption spectra of 15 nm, 102 nm and 198 nm gold NP showed lambda(max) at 520 nm, 535 nm and 577 nm, respectively. SEM study revealed spherical morphology of NP. Gold NP showed size dependent permeation through rat skin and intestine. 15 nm gold NP showed higher permeation compared to 102 nm and 198 nm gold NP. Interestingly, 102 nm and 198 nm gold NP showed lag time of 3h and 6h in case of rat skin only. As the size of the gold NP increased, permeability coefficient and diffusion coefficient was found to be decreased. The permeation of gold NP through intestine was higher than that of skin. TEM study of rat skin revealed accumulation of smaller size gold NP in deeper region of skin whereas larger particles were observed mainly in epidermis and dermis. Presence of gold inside of rat skin was confirmed by EDS. Gold NP would be an interesting carrier for transdermal as well as for oral delivery. The study demonstrated initial proof of concept of percutaneous permeation of smaller size gold particles.