Somatic mutation as an index of in vivo T-cell amplification is a powerful tool to analyze the specificity and size of the autoreactive T-cell repertoire. Using this strategy, we determined the precursor frequency of T cells reactive to myelin basic protein (MBP) and overlapping MBP peptides spanning regions p84-168 in patients with MS and controls in the HPRT mutant T-cell population. Among 19 MS patients, nine had estimatable frequencies to MBP or MBP peptides, p93-112, p124-142 and p143-168 in the HPRT mutant T-cell population. Only one of the 10 controls showed measurable frequency to MBP in the HPRT mutant T-cell population. These studies suggest that increased frequency of T cells reactive to MBP and MBP peptides might indicate putative disease-related epitopes in MS.