The Human Genome Variation Society annual scientific meeting was held on 26 October 2004 in Toronto, Canada, and attracted 85 registrants. Meeting participants from 14 countries reported on the recent advances and progress made toward the detection, analysis, and documentation of genetic variation. Reports were made on improvements to software that can enable curators to create mutation databases that are uniform and are therefore more widely used and easy to distribute. Other reports on software included databases to create haplotypes, predict pathogenic mutations, and compile information on mutations from various sources including relevant clinical data. Improvements to methods for the identification of functional SNPs were reported. New mutation detection methods and methods to identify the effect of a mutation on phenotype were also presented. This meeting report summarizes these presentations.