Modified Atkins diet (MAD) is a less restrictive variety of the classical ketogenic diet (KD), used for treating patients with medically resistant epilepsy. There are only few reports comparing the two types of diets in terms of seizure reduction and tolerability. We compared the effect of a MAD evaluated prospectively on 33 consecutive children with medically resistant epilepsy, with a group of 50 patients, previously treated with KD. Patients who had >50% seizure reduction were considered responders. After 3 months on the MAD, 17 patients (52%) were responders, including 14 (42%) who had >90% seizure reduction. After 6 months, 13 patients (39%) were responders. Seventeen patients (52%) remained on the MAD at least 12 months with excellent overall tolerance and compliance, including 9 patients (27%) who were responders, 4 of them (12%) having >90% seizure reduction. Although there was a trend for higher incidence of responders in the KD group, this failed to reach the level of significance: after 6 months 39% on MAD and 60% on KD were responders. However, this trend was not observed when the two groups were adjusted for difference in age (patients in the MAD group were older than the KD group). In conclusion, our experience suggests that the MAD is similarly effective as the KD in reducing seizure frequency in children with medically resistant epilepsy.