Automation for genotyping of single nucleotide polymorphisms (SNPs) can be split into the automation of the sample preparation and the automation of the analysis technology. SNP genotyping methods are reviewed and solutions for their automation discussed. A panacea for SNP genotyping does not exist. Different scientific questions require adapted solutions. The choice of a technology for SNP genotyping depends on whether few different SNPs are to be genotyped in many individuals, or many different SNPs are to be genotyped in few individuals. The requirements of throughput and the ease of establishing an SNP genotyping operation are important, as well as the degree of integration. The potential and state-of-the-art of different solutions are outlined. Hum Mutat 17:475–492, 2001. © 2001 Wiley-Liss, Inc.