Although negative blood oxygen level-dependent (BOLD) signal changes are very frequent findings in neuroimaging studies of neuronal networks underlying interictal epileptiform discharges (IEDs), the nature of negative BOLD effects in epilepsy remains unclear. To investigate the influence of sleep on BOLD responses to internal activity such as IED, hemodynamic changes associated with IED were analysed in sleep stages 1 and 2 in four children with focal epilepsies who underwent simultaneous EEG-fMRI recordings. There were significantly more voxels with negative BOLD responses and better fit of the expected with the real course of BOLD signal for the negative BOLD effect in sleep stage 2 compared to stage 1. Moreover, the increase in omega (12.0-14.0Hz) and delta (0.5-4.0Hz) power correlated with an increase in the number of deactivated voxels. This study indicates that the second stage of sleep seems to be associated with an increase in negative BOLD response to internal activity compared with sleep stage 1. An increase in inhibitory influences during sleep and decrease of sleep-associated, energy-consuming processes may be responsible for the described negative BOLD signal changes.