We studied 58 splicing mutations originating in vivo at the hypoxanthine guanine phosphoribosyltransferase (HPRT) locus in T-cells of 30 nonsmoking males. A nonrandom distribution of skipped exons was seen after cDNA sequence analysis, with 71% involving exons 2-3 (15), 4 (11), and 8 (15). The mutations likely to have caused the aberrant splicing were identified in 36 mutants by genomic sequencing. The most frequently observed mutations were simple base substitutions (27) and small deletions (7). Among the base substitutions, 23 occurred in the splice consensus sequences, mainly at the highly conserved dinucleotides (21), and preferentially in the acceptor sites (15). The remaining four base substitutions occurred in the coding sequence where one tandem base substitution, one single bp insertion, and two single bp deletions were also observed. The predicted change in three of the base substitutions would be a stop codon. The tandem mutation (CC --> TT) occurred at position 550-551, a possible hotspot for splicing mutations (five of nine previously reported base substitutions at position 551, all C --> T, resulted in abnormal splicing). Four of the base substitutions were new HPRT mutations, two in splice sites (IVS7-3T --> G and IVS8 + 3A --> C) and two in the coding sequence (307A --> T and 594C --> G). All the small deletions (> 1 bp) affected the acceptor sites. The only three identified mutations related to skipping of exons 2 and 3 were located within exon 3, suggesting a frequent involvement of unknown splicing elements distant from these exons.