Liquid chromatography-tandem mass spectrometric assays were developed for the sensitive, rapid and high throughput bioanalyses of thalidomide in human plasma and semen. The matrices were first stabilized with 0.025 M Sorensen's citrate buffer at pH 1.5 to prevent spontaneous hydrolysis. Buffered thalidomide was stable when stored at room temperature for 24 h and for up to three freeze-thaw cycles. Samples were extracted using SPE cartridges. Extracts were then injected into the LC-MS-MS equipped with a reversed-phase column and an APCI interface in the negative ion mode. Calibration curves for both matrices were linear with r>0.99 from 2 to 250 ng/ml and ng/g. Inter-assay precision (RSD) of plasma and semen calibration standards were 2.6-11.6 and 1.9-12.4%, respectively. Recoveries from plasma and semen were greater than 69 and 78%, respectively. Batch sizes of 100 samples per matrix were analyzed with a total run time of 5 h. The methods successfully determined concentrations of thalidomide from a clinical study to levels as low as 7 ng/ml plasma and 8 ng/g semen, respectively.