Background: Epilepsy, febrile convulsion, and breath-holding spells are neurological diseases affecting the heart. Objectives: This study aimed to evaluate electrocardiography alterations in children with epilepsy, febrile convulsion, and breath-holding spells compared to controls. Methods: This case-control study was conducted on 360 children aged 0.5 - 5 years in Zahedan, Iran. The children with epilepsy, febrile convulsion, and breath-holding spells were diagnosed by a single neurologist based on the standard definition. Electrocardiography was also performed by a pediatric cardiologist. The data were analyzed using the SPSS 20.0 software, and P < 0.05 was considered statistically significant. Results: Among the participants, 160 (44.4%) were female. Females also comprised 45.6%, 42.2%, 38.9%, and 51.1% of the participants in the epilepsy, febrile convulsion, breath-holding spells, and control groups, respectively. QTd was different in the epilepsy group compared to the controls and patients with breath-holding spells (P < 0.001). Additionally, QTc was significantly different in the epilepsy group in comparison to the controls (P < 0.001) and patients with breath-holding spells (P - 0.020), in the controls compared to the patients with febrile convulsion (P < 0.001), and in the controls in comparison to the patients with breath-holding spells (P < 0.001). QTcd was also different in the epilepsy group compared to the controls (P < 0.001), patients with breath-holding spells (P < 0.001), and those with febrile convulsion (P = 0.006) as well as in the controls in comparison with the patients with febrile convulsion and breath-holding spells (P < 0.001). Finally, QT was different in the patients with breath-holding spells compared to those with epilepsy (P = 0.005), in the patients with breath-holding spells in comparison with the controls (P = 0.002), and in the patients with breath-holding spells compared to those with febrile convulsion (P < 0.001). Conclusions: The present study findings indicated that QT dispersion was different in the epilepsy group compared to the patients with breath-holding spells, corrected QT was different in the epilepsy group compared with the patients with breath-holding spells, QTc dispersion was different in the epilepsy group in comparison with the patients with breath-holding spells and febrile convulsion, and QT was different in the patients with breath-holding spells compared to those with epilepsy and febrile convulsion.