Motorola is developing a high-throughput, single nucleotide polymorphism (SNP) analysis system which is based on microarrays of raised, hydrophilic gel pads. This three-dimensional microarray system offers distinct advantages over flat microarrays, including a well-characterized, covalent linkage of probes to the gel polymer and a diversity of functional groups available for biomolecule attachment, within an aqueous microenvironment, which is conducive to enzymatic activity. The SNP analysis system assays the DNA polymerase-mediated extension of an anchored oligonucleotide probe which is hybridized to a polymorphic site in an amplified target DNA sample. Assays are analysed for fluorescence signal in a confocal laser slide scanner. This SNP scoring system is currently being used to genotype a population of 1,000 individuals within a larger effort to identify genetic determinants of obesity-related phenotypes in humans. We will presented data to illustrate both the overall performance of this SNP genotyping system, as well as specific results from this pilot study.