Monte Carlo (MC) simulation provides a flexible and robust framework to efficiently evaluate and optimize image processing methods in emission tomography. In this work we present Brain-VISET (Voxel-based Iterative Simulation for Emission Tomography), a method that aims to simulate realistic [99mTc]-SPECT and [18F]-PET brain databases by including anatomical and functional information. To this end, activity and attenuation maps generated using high-resolution anatomical images from patients were used as input maps in a MC projector to simulate SPECT or PET sinograms. The reconstructed images were compared with the corresponding real SPECT or PET studies in an iterative process where the activity inputs maps were being modified at each iteration. Datasets of 30 refractory epileptic patients were used to assess the new method. Each set consisted of structural images (MRI and CT) and functional studies (SPECT and PET), thereby allowing the inclusion of anatomical and functional variability in the simulation input models. SPECT and PET sinograms were obtained using the SimSET package and were reconstructed with the same protocols as those employed for the clinical studies. The convergence of Brain-VISET was evaluated by studying the behavior throughout iterations of the correlation coefficient, the quotient image histogram and a ROI analysis comparing simulated with real studies. The realism of generated maps was also evaluated. Our findings show that Brain-VISET is able to generate realistic SPECT and PET studies and that four iterations is a suitable number of iterations to guarantee a good agreement between simulated and real studies.