Secondary carnitine deficiency may occur in same diseases including malnutrition. The present study examined the serum carnitine levels of children with cancer and their relationship with nutritional status. Fifty-one (mean age: 104 +/- 23 months) patients with cancer were evaluated at diagnosis and 3 months after the initiation of the treatment. There were significant differences between the mean carnitine levels of patients before and during the treatment (p: .004). Although initial carnitine levels of patients were similar to those in control groups, there was a significant difference between the mean carnitine levels of patients and those of the control group at the third month (p: .02). The prevalence of malnutrition at the third month of the treatment (43%) was higher from the prevalence at diagnosis (33 %) but this was not significant. No significant relationship was found between carnitine levels and nutritional status of patients either at diagnosis or during treatment. These results showed that inadequate intake of carnitine or its precursors could not be responsible for decrease in carnitine levels. Metabolic changes that result from therapy and/or from neoplastic process may be responsible for the decrease in carnitine levels. Detailed studies, including measurements of fractions of carnitine and urinary carnitine excretion according to individual drug, are necessary to determine real cause of this decrease.