A simple and rapid PCR-based method has been developed for determining the genotype of seeds before germination. Single half-seeds of rice (Oryza sativa L.) and wheat (Triticum aestivum L. em. Thell.) were preincubated, without grinding, in an aqueous extraction buffer. The resulting supernatants were then used in polymerase chain reaction (PCR) with oligonucleotide primers corresponding to rice single-copy sequences or a wheat microsatellite repeat. PCR products of identical size were amplified using either the half-seed extract or DNA isolated from leaf tissue. The remnant half-seeds can be maintained in ordered arrays using microtiter plates allowing the recovery of selected genotypes. Pre-germination genotypic screening of seed populations as described in this report should be useful for a variety of applications in plant breeding and genetics studies.