The alkaline single cell gel (SCG) assay is a sensitive electrophoretic technique for detecting the presence of DNA single strand breaks and alkali-labile damage in individual cells. This technique was used to assess and compare the level of DNA damage in peripheral blood leukocytes/lymphocytes from well-nourished children with infection, well-nourished children with infection and under drug treatment, and from malnourished infected children with and without previous drug treatment. The present study shows that severe infection is associated with a significant increase in DNA damage. The average migration length was five times greater in severely infected well-nourished children compared to that found in healthy, well-nourished children. The results obtained in this study indicate that malnutrition is another factor associated with an increase in DNA migration. The average tail length for malnourished, severely infected children was twice as great as that obtained for cells from well-nourished, severely infected children. We also detected a variable increase in DNA migration associated with treatment for severe infection. Nevertheless, the excessive heterogeneity, the concurrent number of drugs used and the limited size of the treated population precludes an accurate assessment of which drugs were involved in the increase in DNA damage. Further studies will be necessary involving a large number of patients to address the relation between levels of DNA damage and specific kinds of infection, various drug treatments, and the type and severity of malnutrition. The increased level of DNA damage in severely infected and malnourished children could be related to negative effects such as a deficient immune response resulting in an increased susceptibility to malignant transformation.