Among the many clinical applications of the polymerase chain reaction (PCR) is its potential use in preimplantation diagnosis of genetic disorders. Performing PCR on single blastomeres from early cleavage stage (six- to eight-cell) human embryos should, in principle, enable reliable determination of disease status for certain inherited conditions. However, reports of misdiagnoses using this technique have diminished enthusiasm for its widespread clinical use. One principal source of error is the propensity for genome-targeted PCR to exclusively amplify one allele in reactions assaying a single heterozygous diploid cell. Complete reaction failure is also common. Employing the Marfan syndrome (MFS) as a paradigm, we have developed a reliable, reverse transcription-PCR-based method of genotyping single cells that overcomes these obstacles. The technique should facilitate accurate preimplantation diagnosis of MFS and other selected genetic diseases caused by heterozygous or compound-heterozygous mutations.