The use of automated DNA fragment analysis with the Applied Biosystems 672 Genescanner system was evaluated in a routine diagnostic setting. The aim of the study was to compare automated fragment detection and analysis with conventional methods. For cystic fibrosis analysis the delta F508 mutation in exon 10 of the cystic fibrosis transmembrane regulator (CFTR) gene was multiplexed with two intragenic microsatellites. The analysis of the Prader-Willi/Angelman region of chromosome 15 used a panel of five microsatellites. For dystrophin, seven microsatellites covering the entire dystrophin gene were co-amplified. Automated analysis was faster and more accurate than analysis using radiolabelled products with sequencing gels, although some inconsistencies in the sizing of microsatellite alleles were seen.