BACKGROUND:The challenge in systematic toxicological analysis using gas chromatography and/or liquid chromatography coupled to mass spectrometry is to identify compounds of interest from background noise. The large amount of spectral information collected in one full-scan MS run demands the use of automated evaluation of recorded data files. We evaluated the applicability of the freeware deconvolution software AMDIS (Automated Mass Spectral Deconvolution and Identification System) for GC-MS-based systematic toxicological analysis in urine for increasing the speed of evaluation and automating the daily routine workload.