Skin is the largest organ of the body and is a potential route of exposure to sunscreens and cosmetics containing nanoparticles, but the permeability of the skin to these nanoparticles is unknown. In this paper, we studied the transdermal delivery capacity through mouse skin of water-soluble CdSeS quantum dots (QDs) and the deposition of these QDs in the body. QD solution was coated on the dorsal hairless skin of male ICR mice. Fluorescence microscope was used to observe the deposition of QDs in mouse skin and heart, liver, spleen, lung and kidney. Inductively coupled plasma-mass spectrometry (ICP-MS) was used to measure the ¹¹¹Cd concentration to indicate the concentration of QDs in plasma and organs. The fluorescence images show that QDs can penetrate into the dermal layer and deposit in the organs through blood circulation. ICP-MS result indicates that QDs deposit seriously in liver and kidney, and they are difficult to clear. ¹¹¹Cd concentration is still more than 14 ng/g in kidney after 5 days. These results suggest that QDs has in vivo transdermal delivery capacity through mouse skin and is harmful to the liver and kidney.