In this study, cranial magnetic resonance imaging (MRI) findings were investigated in children with moderate and severe protein energy malnutrition (PEM) to determine cerebral abnormalities in malnutrition in childhood. A total of 20 children aged 3 months to 36 months were included in the study. Thirteen (65%) children had severe malnutrition and seven (35%) children had moderate malnutrition. Fifteen (75%) children had abnormal MRI findings: all of them had cerebral atrophy, and 10 (75%) children had cerebral atrophy plus ventricular dilatation. None of the children had abnormality in the brain stem or cerebellum. The authors did not find statistically significant differences between the groups when comparing the MRI findings for degree of malnutrition, head circumference, iron deficiency anemia, and serum albumin levels. In conclusion, the findings showed that most (75%) children with moderate/severe PEM had abnormal MRI findings. Therefore, it is suggested that children with PEM should be evaluated for cerebral atrophy.