Summary Objective Zinc, copper and selenium are essential for normal development and function of the central nervous system. This study aimed at assessment of serum levels of zinc, copper and selenium in children with severe acute malnutrition (SAM) with & without cerebral palsy both before and after nutritional rehabilitation. Methods A prospective case control study involved 2 groups (Group I); included160 children with SAM of both sex, aged 6–59 months, this group was subdivided into 2equal subgroups; subgroup A: SAM without cerebral palsy, subgroup B: SAM with cerebral palsy. Group II (control group) included 96 apparently healthy children matching age and sex with the first group. Both groups were subjected to a detailed history including nutritional history. Anthropometric measurements were recorded and laboratory assessment for serum levels of (copper, zinc, & selenium) before and after nutritional rehabilitation were performed for all children. Results Group I (A&B) showed a significant decrease in anthropometric measurements, serum zinc, serum selenium but normal copper level before nutritional rehabilitation in comparison to control. After nutritional rehabilitation, all cases of the group I showed a significant improvement of the three parameters except for (45%) of cerebral palsy cases, experienced a resistant low selenium. Conclusion Nutritional rehabilitation significantly improved micronutrients' serum level in SAM children with and without cerebral palsy. Selenium supplementation is advised for children with cerebral palsy in order to reach normal values with observation of effect on neurological state.