Both an excess of iron and iron deficiency (ID) may lead to significant cardiac problems. Parameters that represent ventricular repolarization heterogeneity, like QT dispersion (QTd), corrected QT dispersion (QTcd), the interval between the peak and the end of the T wave (Tp-e), and Tp-e dispersion, have not been evaluated in otherwise healthy children with low iron levels before. Here we assessed the effects of low iron storage on P wave dispersion (PWd), QTd, Tp-e intervals, and Tp-e dispersion in otherwise healthy children. We prospectively reviewed 283 patients who were referred to pediatric cardiology department for cardiac evaluation due to murmurs and who were found to have no structural heart disease. The patients were divided into three groups according to their ferritin levels: Group 1: ferritin < 15 ng/mL (n = 58); Group 2: ferritin 15-25 ng/mL (n = 80); Group 3: ferritin > 25 ng/mL (n = 145). P wave duration (PW), QT and Tp-e intervals, and PW, QT, corrected QT (QTc), and Tp-e dispersions were significantly higher in patients whose ferritin level was < 15 ng/mL. A negative correlation was found between ferritin level and QT and QTc intervals, and QT, QTc, and Tp-e dispersions. Our results showed that a low serum ferritin level is associated with changes in some ECG parameters such as prolonged PWd, Tp-e interval, QT, QTc, and Tp-e dispersions in otherwise healthy children, and studies of other populations indicated that these parameters may predict arrhythmias in selected patients. These patients may be considered at some risk of developing arrhythmias. Therefore, careful evaluation of these ECG parameters is necessary in otherwise healthy children with low iron stores.