The skin is the largest organ of the body and is a potential route of exposure to sunscreens and cosmetics containing nanoparticles; however, the permeability of the skin to these nanoparticles is currently 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 onto the dorsal hairless skin of male ICR mice. Fluorescence microscopy and transmission electron microscopy (TEM) were used to observe the distribution of QDs in the skin and organs, and inductively coupled plasma-mass spectrometry (ICP-MS) was used to measure the (111)Cd content to indicate the concentration of QDs in plasma and organs. Experimental results indicate that QDs can penetrate into the dermal layer and are limited to the uppermost stratum corneum layers and the hair follicles. Through blood circulation, QDs deposit mostly in liver and kidney and are difficult to clear. (111)Cd concentration was greater than 14 ng g(-1) in kidney after 120 h after 0.32 nmol QDs was applied to a mouse. These results suggest that QDs have in vivo transdermal delivery capacity through mouse skin and are harmful to the liver and kidney.