Aim: The aim is to compare the markers of oxidative stress in iron deficient children to that of non-anemic children. Method: Serum thiol-disulfide level, ferroxidase activity and ischemia-modified albumin (IMA) levels were compared between iron deficiency anemia (IDA) and non-anemic children. Results: A total of 117 children, 66 with IDA and 51 non-anemic children were included in the study. Disulfide, disulfide/native thiol, and disulfide/total thiol levels were significantly higher in the IDA group (p: 0.001). Serum ferroxidase levels were significantly lower in the IDA group (p: 0.04); but there was no significant difference between the two groups regarding serum IMA levels (p: 0.42). There was a weak negative correlation between disulfide and serum hemoglobin (p: 0.004), iron (p: 0.041), and ferritin (p: 0.023) levels while there was a weak positive correlation between ferroxidase activity and these parameters. Conclusion: There is an increased protein oxidation in children with IDA compared with non-anemic controls.