The present invention provides a microarray for detecting a genotype at a polymorphic site in a plurality of nucleic acid samples, comprising a first set of nucleic acid fragments derived from the samples and a second set of nucleic acid fragments derived from a plurality of references immobilized thereon. The invention also provides a microarray comprising a set of nucleic acid fragments immobilized on the surface of the microarray, wherein the nucleic acid fragments are derived from the samples by amplifying a region in the sample containing the polymorphism through asymmetric PCR amplification. Methods of using and making the microarrays are also provided.