Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) is one of the most important proteomic technologies currently available for the high-throughput analysis of complex protein samples. In the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis, particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding of the limitations of this technology and the pitfalls in biomarker discovery. Bearing these limitations in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the preanalytical and analytical phases and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false significant results, studies have to be carefully designed and control groups have to be accurately selected. In addition, data should be analyzed with appropriate tools already established for analysis of highly complex microarray data. Finally, validation of the significance of any biomarker candidate derived from pilot studies is mandatory in appropriately designed prospective multi-centre studies; the reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required and few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.