Background : Surface-enhanced laser desorption-ionization time-of-flight (SELDI-TOF) mass spectrometry of human serum is a potential diagnostic tool in human diseases. In the present study, the preanalytical and analytical variation of SELDI-TOF mass spectrometry of serum was assessed in healthy individuals. Methods : Serum and plasma were obtained from healthy human individuals. Protein peaks in human serum and plasma were determined by SELDI-TOF mass spectrometry. Results : The protein peaks in serum in healthy individuals showed no variation with gender, age, fasting, or diurnal rhythm. The intensity of protein peaks changed significantly during clotting of serum from 30 to 60min, followed by smaller changes from 60 to 120min. The intensity of protein peaks changed after 60-min storage of serum at room temperature, whereas no changes were observed for storage on ice. The number of reproducible protein peaks in serum was determined on WCX2, SAX2, and IMAC30 arrays as 29, 34, and 36, respectively. The average coefficient of variation (CV) of the mass value of protein peaks was 0.03%. The intra-assay CV of peak intensity on IMAC30 arrays was 16% (10%–36%, n=8) for 36 peaks, inter-assay CV was 18% (6%–34%, n=4) for 16 peaks, and inter-individual CV was 38% (16%–56%, n=16) for 20 peaks. Conclusions : The pre-analytical and analytical conditions of SELDI-TOF mass spectrometry of serum have a significant impact on the protein peaks, with the number of peaks low and the assay variation high. Consequently, SELDI-TOF mass spectrometry of serum needs further evaluation before application in clinical diagnostics. Clin Chem Lab Med 2006;44:1243–52.