We analyzed DNA from 13 males with ornithine transcarbamylase (OTC) deficiency for gene deletions and known point mutations using the polymerase chain reaction (PCR), allelle-specific oligonucleotide (ASO) hybridization, and Southern blotting with full-length OTC cDNA and exon-specific probes. Three patients were found to have deletions: one was missing the whole OTC gene; a second patient had a deletion of both exon 7 and 8; and the third had a deletion of exon 9. Only one of the remaining 10 patients had a known point mutation consisting of a G-to-A change in nucleotide 422 of the sense strand resulting in a glutamine substitution for arginine at amino acid 109 of the mature OTC protein. This study describes the integration of various molecular methods to screen OTC-deficient patients for deletions and points mutations. Two new deletions within the OTC gene are described.