Prenatal X-irradiation, even at doses <1 Gy, can induce spatial disarray of neurons in the brains of offspring, possibly due to disturbed neuronal migration. Here we analyze the effects of prenatal low-dose X-irradiation using a novel stereological method designed to investigate the three-dimensional (3D) spatial arrangement of neurons in thick sections. Pregnant mice were X-irradiated with 50 cGy on embryonic day 13 or were sham-irradiated. The right brain halves of their 180-day-old offspring were dissected into entire series of 150 microm thick frontal cryostat sections and stained with gallocyanin. Approximately 700 layer V pyramidal cells per animal were sampled in a systematic-random manner in the middle of the section's thickness. The x-y-z coordinates of these 'parent neurons' were recorded, as well as of all neighboring (up to 10) 'offspring neurons' close to each 'parent neuron'. From these data, the nearest neighbor distance (NND) distributions for layer V pyramidal cells were calculated. Using this novel 3D analysis method, we found that, in comparison to controls, prenatal X-irradiation had no effect on the total neuron number, but did cause a reduction in the mean volume of layer V by 26.5% and a more dispersed spatial arrangement of these neurons. Considering the recent literature, it seems reasonable to consider abnormal neuronal migration as the potential basic cause of this finding.