Amplified alleles at the PLA2 short tandem repeat locus were sequenced and analyzed using different combinations of the PCR primer. When changing one side of the primers from the previous design to the researchers' original one, additional alleles, which had been previously hidden, could be newly detected in two of sixty DNA samples of unrelated Japanese individuals. The sequence data revealed both hidden alleles to be accompanied by a 3-bp deletion in the 5'-flanking region of the trimeric short tandem repeat. The position of the deletion corresponded to the exact 3' end of the primer, which had been formerly used. In the present case, both of the base numbers, which constituted the core repeat unit and which were deleted in the hidden alleles, were equal. Therefore, it was impossible to distinguish an allele from that with not only an additional trimeric repeat but a 3-bp deletion without the sequence analysis. This result indicated that the estimated allele size does not always reflect the difference in the repeat number even if the alleles regularly differ in size by one repeat unit. Moreover, this study suggested the presence of apparent homozygotes, of which the fellow of the heterozygous alleles is hidden by an unsuccessful amplification due to the sequence variation. Figures, references