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With the rapid development of quantum dot (QD) technology, water-soluble QDs have the prospect of being used as a biological probe for specific diagnoses, but their biological behaviors in vivo are little known. Our recent in vivo studies concentrated on the bio-kinetics of QDs coated by hydroxyl group modified silica networks (the QDs are 21.3 ± 2.0 nm in diameter and have maximal emission at 570 nm). Male ICR mice were intravenously given the water-soluble QDs with a single dose of 5 nmol/mouse. Inductively coupled plasma-mass spectrometry was used to measure the 111Cd content to indicate the concentration of QDs in plasma, organs, and excretion samples collected at predetermined time intervals. Meanwhile, the distribution and aggregation state of QDs in tissues were also investigated by pathological examination and differential centrifugation. The plasma half-life and clearance of QDs were 19.8 ± 3.2 h and 57.3 ± 9.2 ml/h/kg, respectively. The liver and kidney were the main target organs for QDs. The QDs metabolized in three paths depending on their distinct aggregated states in vivo. A fraction of free QDs, maintaining their original form, could be filtered by glomerular capillaries and excreted via urine as small molecules within five days. Most QDs bound to protein and aggregated into larger particles that were metabolized in the liver and excreted via feces in vivo. After five days, 8.6% of the injected dose of aggregated QDs still remained in hepatic tissue and it was difficult for this fraction to clear.