The discrepancy of results for the quantification of androstenedione in human serum between a radioimmunoassay (RIA) method and high performance liquid chromatography tandem-mass spectrometry (LC-MS/MS) was investigated. RIA overestimated concentrations compared to LC-MS/MS on 59 clinical samples (RIA=1.79×LC-MS/MS+0.94). RIA kit and LC-MS/MS calibrants were also determined by both methods. The RIA performed with improved accuracy on the calibrants (RIA=1.35×LC-MS/MS-0.28). Lipid, protein, electrolyte content, and pH of the two sets of calibrants were further investigated. The RIA calibrants contained little lipid material, while the LC-MS/MS calibrant material contained the same levels expected in normal serum/plasma. The pH and sex hormone binding globulin (SHBG) values were different between the RIA calibrants and the LC-MS/MS calibrant material (SHBG, 31±2 and 38±2nmol/l; pH, 8.27±0.18 and 8.66±0.03, respectively). No correlation was observed between androstenedione RIA and LC-MS/MS discrepancy and lipid or protein. LC-MS/MS sample preparation was tested for the removal of protein-bound material and recovery determined (99-108%). The corresponding RIA results overestimated androstenedione by 52-174% compared to LC-MS/MS. The results here demonstrate that LC-MS/MS is the more accurate method.