Background Voxel-based morphometric (VBM) studies in neuromyelitis optica (NMO) have shown limited reproducibility. A previous study suggests that the number of optic neuritis (ON) attacks may be a confounding factor when comparing NMO patients with controls if it is not taken into account during VBM analysis. Purpose To investigate the potential confounding effect of the number of ON attacks, for both tissue volumes and perfusion by voxel-based statistical analysis. Material and Methods Volumetric magnetic resonance imaging (MRI) and perfusion SPECT were obtained from 15 controls and two patient subgroups: subgroup I was composed of nine patients with one or two ON attacks; and subgroup II of six patients with three or four ON attacks. We performed non-parametric voxel-based comparison of tissue volumes and perfusion between controls versus the two patient subgroups and for the whole patient group. Results Subgroup I presented no volume reductions, contrary to subgroup II that showed unequivocal reduction. We also found hypoperfusion in different brain regions in different subgroups. The results were quite different for the whole patient group. Conclusion These findings highlight the confounding effect of the number of ON attacks, providing a new methodological insight that could explain the limited reproducibility of previous VBM studies in NMO.