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To assess the anatomic variation and age-related changes of phase shifts in the neonatal cerebral venous system at susceptibility-weighted imaging (SWI).Thirty-five neonates who had undergone SWI and who did not have any intracranial or systemic abnormalities were retrospectively assessed. Phase shifts in the veins in the deep gray matter and in the cortical veins in the frontal, rolandic, and parietal areas were measured and compared. Correlations between phase ratio (ratio of the phase shift in the vein in the deep gray matter to that in the cortical veins) and gestational age at birth, gestational age at magnetic resonance imaging (MRI), and age after birth were assessed.Phase shift in the veins in the deep gray matter was significantly higher than those in the cortical veins (P < 0.01). Among the cortical veins, the venous phase shift in the rolandic area was significantly higher than those in the frontal and parietal areas (P < 0.01). There was a negative correlation between the phase ratio and the gestational age at MRI (Spearman ρ = −0.35, P = 0.04).An anatomical variation in phase shifts was identified in the neonatal venous system. The observed reduction in phase shift differences between the veins in the deep gray matter and those in the cortex as gestational age at MRI increased may reflect brain development. J. Magn. Reson. Imaging 2011;. © 2011 Wiley Periodicals, Inc.