The present study attemps to investigate the impact of protein-energy malnutrition (PEM) on chromosomal abnormalities in children. Sixty-seven children suffering from marasmus, marasmic-kwashiorkor, and kwashiorkor were chosen from the inpatient Pediatric Department of Medical Faculty of Ataturk University. They were matched by age, sex,and socioeconomic status to twenty-five health children (control). After 72 hours, 100 cultured lymphocyte cells from each subject were analyzed. The frequency of chromosome abnormalities was found to be nearly nine time greater among children with PEM compared to controls (12.59% versus 1.24% respectively); the difference was statistically highly significant, p<0.001. The abnormalities were mainly gaps, isogaps, chromatid breaks, chromosome breaks, dicentric chromosomes, acentric chromosomes,and fragments. Ring chromosomes were not observed. We found an inverse correlation between gap incidence and both total protein and albumin level (r:-0.380 p<0.005, r:-0.391 p<0.005 respectively).