Abstract: Methods and kits are provided for genotyping a plurality of pre-selected SNPs. For each SNP a pair of oligos is synthesized. Each oligo is a perfect match to one allele of a polymorphic locus. The oligos are hybridized to genomic DNA and only those that are a perfect match to an allele that is present will hybridize. The hybridization reaction is size separated so that unbound oligos go with the small size fraction and bound oligos go with the large size fraction. The oligos in the large size fraction are amplified and detected to determine the genotype of the sample.