During the last years, mass spectrometry has revolutionised protein biochemistry and has advanced to a superior tool for the identification and detailed analysis of peptides and proteins. The high throughput allowed by some mass spectrometry platforms has enabled the important step from analysis of individual proteins to proteomics. Recently, an additional field of mass spectrometry applications has emerged - namely screening and diagnostic research. In contrast to protein identification, screening applications have to detect analyte molecules of defined molecular weights which can be calculated beforehand, for example by means of chemical structures. Here, the accuracy and sensitivity of mass spectrometry has to be combined with the requirements of high-throughput analyses, in particular speed and automation. These criteria are especially fulfilled by state of the art matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) instruments. The first high throughput screening (HTS) application proved to be genotyping of single nucleotide polymorphisms. The same principle was later applied for several quality control issues, for example for oligonucleotides, peptide or compound libraries. This development has culminated in the screening and profiling of complex biomarker patterns in clinical proteomics to detect a molecular fingerprint for specific diseases in biological samples. Thus, mass spectrometry based methods are expected to enable a very early diagnosis of diseases with minimally invasive methods of investigation. This type of high end screening application has the potential to revolutionise the early diagnosis of many diseases. Here, we give an overview of the application of mass spectrometry in the fields of screening and diagnostic research.