Simultaneous recording of EEG and functional MRI (EEG-fMRI) is a promising tool that may be applied in patients with epilepsy to investigate haemodynamic changes associated with interictal epileptiform discharges (IED). As the yield of the EEG-fMRI technique in children with epilepsy is still unclear, the aim of this study was to evaluate whether the combination of EEG-fMRI and EEG source analysis could improve localization of epileptogenic foci in children. Six children with an unambiguous focus localization were selected based on the criterion of the consistency of ictal EEG, PET and ictal SPECT. IEDs were taken as time series for fMRI analysis and as averaged sweeps for the EEG source analysis based on the distributed linear local autoregressive average (LAURA) solution. In four patients, the brain area with haemodymanic changes corresponded to the epileptogenic zone. However, additional distant regions with haemodynamic response were observed. Source analysis located the source of the initial epileptic activity in all cases in the presumed epileptogenic zone and revealed propagation in five cases. In three cases there was a good correspondence between haemodynamic changes and source localization at both the beginning and the propagation of IED. In the remaining three cases, at least one area of haemodynamic changes corresponded to either the beginning or the propagation. In most children analysed, EEG-fMRI revealed extended haemodynamic response, which were difficult to interpret without an appropriate reference, i.e. a priori hypothesis about epileptogenic zone. EEG source analysis may help to differentiate brain areas with haemodynamic response.