Sister chromatid exchanges (SCE) and lymphocyte subsets of children with acute lymphoblastic leukemia (ALL) were investigated in children with ALL during chemotherapy and at least 5 years after chemotherapy. The treatment of the new admitted patients followed protocol ALL-BFM-90. Children with ALL at the time of diagnosis showed statistically significant higher SCE frequencies (4.9 +/- 0.77) than healthy controls (3.6 +/- 0.93; p = 0.002). The in vivo effects of cyclophosphamide (CP) resulted in a dramatic increase of the SCE frequency (20.5 +/- 3.76). This increased SCE level of lymphocytes might reflect an instability of DNA or a deficiency of DNA repair capacity. However, immediately one week after the administration of CP, the SCE rate decreased. This decline of SCE frequency correlates with a severe reduction of the absolute numbers of T lymphocytes. The observed reduction of SCE frequency may be due to a depletion of T lymphocytes, or a repair of DNA. The patients in long term remission ( > 5 years) have had the therapy according BFM-83 (9 pat.) and modified 'Pinkel-regime' (2 pat.). No difference was found between the SCE-rate of the patients in remission and of the age-dependent control group. These results might correlate with the low risk for future development of relaps or second malignancy.