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Objective: Different studies have reported contradictory results regarding the relationship between iron deficiency anemia (IDA) and febrile seizure (FS). The present study was conducted to determine the effect of IDA on FS in children.Patients and Methods: This case-control study was conducted among 52 children with FS (the case group) and 18 children with afebrile seizures and 51 children with fever without seizures in the age range of 6 months to 5 years admitted to the pediatric ward of Imam Khomeini Hospital in Ilam from March 2016 to January 2017. Patients were selected using the convenience sampling method. Red blood cell (RBC) count as well as measurement of hemoglobin (Hb), hematocrit (Hct), ferritin, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration (MCHC) levels were performed in all patients. The collected data were analyzed using SPSS16 software.Results: A total of 34.6% in the FS group, 66.7% in the afebrile seizure group and 41.2% in the fever without seizure group suffered from IDA, which was not statistically significant between the three groups. Hb, Hct and RBC levels were higher in the case group and MCV, MCH, MCHC levels in the case group were lower than those in the control group. The odds ratio (OR) for FS compared to the febrile group was 0.756 [95% confidence interval (CI) = 0.34-1.68; p = 0.493] and that for FS compared to seizure was 0.265 (95% CI = 0.085-0.823; p = 0.022).Conclusions: This study showed that IDA may have protective effects on the onset of FS, and based on the results, IDA is more common in children with afebrile seizures. Further and more comprehensive studies are recommended. [ABSTRACT FROM AUTHOR]