Introduction Nutritional assessment is an essential component of the initial assessment of children with cancer. Malnutrition may be present at diagnosis due to the effects of the malignancy or, in low income countries (LIC), due to poverty and an inadequate diet. Purpose The aim of this study is to evaluate the prevalence of malnutrition at diagnosis in children with cancer in Morocco. Procedure Nutritional status of 100 children aged less than 18 years with newly diagnosed malignancy between January 2005 and January 2006 was evaluated by anthropometric and biochemical parameters before initiating therapy. We measured weight, height, weight-for-height using z-scores index for children and body mass index for adolescents, triceps skinfold thickness and mid-upper arm circumference, and serum albumin. Results A total of 100 patients were included. The mean age was 7 years (range 1 to 18 years). Sixty percent were boys. The diagnosis was: Burkitt lymphoma (n=19), acute myeloblastic leukaemia (n=18), acute lymphoblastic leukaemia (n=14), rhabdomyosarcoma (n=13), Ewing sarcoma (n=7), nephroblastoma (n=6), Hodgkin disease (n=5), osteosarcoma (n=5), retinoblastoma (n=4), neuroblastoma (n=3), germ cell tumor (n=3), orbital lymphoma (n=1), cerebral lymphoma (n=1), ependymoma (n=1). Incidence of malnutrition ranged from 20–50%, depending upon the measurement used. Conclusion The prevalence of malnutrition in this study was high, so interventions are being implemented to improve the nutritional status of these patients.