Advances in nanotechnology research on quantum dots (QDs)—water soluble ZnS-capped, CdSe fluorescent semiconductor nanocrystals—for in vivo biomedical applications have prompted a close scrutiny of the behavior of nanostructures in vivo. Data pertaining to pharmacokinetics and toxicity will undoubtedly assist in designing better in vivo nanostructure contrast agents or therapies. In vivo kinetics, clearance, and metabolism of semiconductor QDs are characterized following their intravenous dosing in Sprague–Dawley rats. The QDs coated with the organic molecule mercaptoundecanoic acid and crosslinked with lysine (denoted as QD-LM) are cleared from plasma with a clearance of 0.59 ± 0.16 mL min–1 kg–1. A higher clearance (1.23 ± 0.22 mL min–1 kg–1) exists when the QDs are conjugated to bovine serum albumin (denoted as QD-BSA, P < .05 (P = statistical significance). The biodistribution between these two QDs is also different. The liver takes up 40 % of the QD-LM dose and 99 % of QD-BSA dose after 90 min. Small amounts of both QDs appear in the spleen, kidney, and bone marrow. However, QDs are not detected in feces or urine for up to ten days after intravenous dosing.