To determine the clinical features that contribute to an increased frequency of mutant T cells (FMC) in patients with systemic lupus erythematosus (SLE). During in vivo T cell division, there are errors in replication which give rise to mutations throughout the genome. An estimate of such mutations may be obtained by focusing on mutations in the hprt gene, which can be screened by assessing relative growth of T cell clones in the presence and absence of 6-thioguanine. In this study, peripheral blood T cell clones from 47 patients with SLE were assessed, and the frequency of mutant T cells (FMC) determined. An attempt was made to correlate the FMC with disease measures. Patients with SLE had a spectrum of FMC values, ranging from normal to almost 1,000 times normal. Total duration of active disease (rs = 0.94), past highest disease activity index (rs = 0.80), and number of lupus flares (rs = 0.76) correlated most strongly (P < 0.0001) with FMC by Spearman's rank order analysis. In contrast, current disease activity index and current anti-DNA level did not correlate with FMC. Similar correlations between FMC and cumulative past lupus disease activity were found by linear regression analysis (rp = 0.89 for the correlation between the natural logarithm of FMC and cumulative duration of active disease). By both statistical tests, therapy was found to be only a minor contributor to FMC. In our patient population, a high FMC value appears to reflect cumulative clinical lupus disease activity, involving both intensity and duration of past active disease.