Malnutrition is a significant problem in paediatric oncology, and carries poor prognosis due to higher toxicity and poor response to treatment in malnourished patients. In this study, we used animal model of early-life moderate malnutrition to assess changes in pharmacokinetics and toxicity of anticancer drugs, and the associated molecular mechanisms. We have found significant metabolomic and proteomic changes in malnourished animals. These changes were found to be correlated with changes in pharmacokinetics and increased toxicity of chemotherapy drugs.