Lysosomal acid lipase (LAL) is a hydrolase essential for the intracellular degradation of cholesteryl esters and triglycerides. We previously reported a rat model of Wolman's disease (Wolman rat) that is deficient for LAL activity. In this study, we cloned rat LAL (RLAL) cDNA and investigated abnormal LAL gene expression in the Wolman rat. We cloned the RLAL gene from a cDNA library made from normal rat liver mRNA using the human LAL cDNA as a probe, subcloned the RLAL cDNA into pBlueScript vector, and sequenced it. Next, we constructed a cDNA library from a Wolman rat liver, and used the RLAL cDNA as a probe to isolate the Wolman RLAL cDNA for comparison. The normal RLAL cDNA contains 3150 bp including an 1194 bp open reading frame and three poly A signals at the 3' end. The deduced amino acid sequence contained 397 amino acids, showed 79.9% homology with human LAL, and had the same functional domains at the same sites as human LAL. Northern blot analysis revealed that the RLAL mRNA from normal rat was 3.2 kb in length, while the RLAL mRNA from Wolman rat was only 1.4 kb. Nucleotide sequence analysis showed that Wolman rat LAL cDNA had the same sequence as a RLAL cDNA from the 5'-untranslated region to nt 1101, followed by a 60 bp replacement from nt 1102 to nt 1161 with poly A signal and a 3' 1.8 kb deletion. The deduced amino acid sequence demonstrated the substitution of 367Ile to Asn, 368Pro to stop codon, and deletion of the C-terminal 29 amino acids. Genomic Southern blot analysis disclosed a large deletion at the 3' end of the gene. These results identify the molecular defect in the Wolman RLAL, and suggest that the C-terminus of RLAL is essential for the activity and/or stability of the enzyme.