The recent popularity of DNA chip technology has been fostered by the increasing demand for new tools, which allow the simultaneous analysis of large numbers of nucleic acid hybridization experiments in a timely fashion. The development of DNA chip-based assays has been strongly driven by modern approaches aiming at the comprehensive analysis of multiple gene mutations and expressed sequences. The broad range of current DNA chip applications include the detection of pathogens, the measurement of differences in the expression of genes between different cell populations as well as the analysis of genomic alterations such as sequence or copy number alterations of disease related genes or single nucleotide polymorphisms. A brief overview of the impact of DNA chip technology on the field of Molecular Medicine will be provided, followed by a more detailed presentation on DNA chip technology for large-scale differential expression profiling.