In addition to the traditional cytogenetics still used as the basic methodology for everyday clinical diagnosis, new molecular cytogenetic techniques provide a useful basis for routine diagnosis. Flourescence in situ hybridization (FISH) has become a standard technique, and comparative genomic hybridization (CGH), spectral karyotyping (SKY), and multi-color FISH have shown their potential for diagnostic purposes. Following a section on tissue culture, chromosome staining and basic information about karyotyping, nomenclature and quality standards, protocols of relevance for comprehensive cytogenetic diagnostics are presented.