In DNA from a male patient of German and Polish ancestry who has lipoprotein lipase deficiency, sequencing of all nine exons and intron-exon boundaries corresponding to the coding region of the lipoprotein lipase gene detected a C----T transition leading to the substitution of a stop signal for the codon that normally determines a glutamine at position 106 of the mature enzyme. Hybridization with allele-specific oligonucleotides at this position established that the patient was homozygous for this mutation. This mutation must lead to the synthesis of a sharply truncated protein, accounting for the enzymatic deficiency noted in the patient.