We have developed an assay for allele-specific determination of low-density lipoprotein receptor (LDLR) mRNAs. Transcript levels are measured by reverse transcription (RT), PCR, and electrophoresis on an automatic DNA sequencer using fluorescence-labeled primers and direct quantitation of the allele-specific RT-PCR products. The discrimination between the allelic products is based on the use of DNA polymorphisms located in the coding regions of the gene as markers for the individual alleles. Using this method on LDLR mRNA from heterozygous patients with familial hypercholesterolemia (FH) due to a defective LDLR protein, it is possible to relate the expression of the mutant allele directly to the expressed amounts of the normal allele, thus overcoming the problems of using artificial internal standards in the PCR. To validate the method we have measured (1) the range of normal LDLR allele transcript levels, and (2) the transcript levels in patients heterozygous for different types of mutant LDLR alleles associated with FH. The method is general in principle and can be applied in the allele-specific analysis of transcripts from all genes harbouring DNA polymorphisms in their coding regions.