We performed a comparison study focusing on differences in fractional anisotropy (FA) and mean diffusivity (MD) between 3-T and 1.5-T diffusion tensor imaging (DTI) with parallel imaging. Thirty healthy volunteers underwent DTI with an eight-channel phased-array coil at both 3 T and 1.5 T. Histogram and region of interest (ROI) analyses were performed. Paired t tests were applied for statistical analysis. Signal-to-noise ratios of these regions were also measured. For histogram analysis, peak location of FA was significantly lower at 3 T than at 1.5 T (P = 0.04). Mean FA was significantly higher at 3 T than at 1.5 T (P = 0.002). Peak location of MD was significantly lower at 3 T than at 1.5 T (P < 0.001). Mean MD was significantly lower at 3 T than at 1.5 T (P < 0.001). In ROI analysis, FA was significantly larger at 3 T than at 1.5 T in the centrum semiovale (P < 0.001), middle cerebellar peduncle (P < 0.001), cerebral peduncle (P = 0.006), posterior limb of the internal capsule (P = 0.007), genu (P < 0.001) and splenium (P < 0.001). FA was significantly lower at 3 T than at 1.5 T in the globus pallidus (P < 0.001). MD was significantly smaller at 3 T than at 1.5 T in the globus pallidus (P = 0.007), thalamus (P < 0.001), centrum semiovale (P < 0.001), middle cerebellar peduncle (P < 0.001), cerebral peduncle (P = 0.01), posterior limb of the internal capsule (P < 0.001), genu (P = 0.01) and splenium (P < 0.001). Significant differences in FA and MD exist between 3 T and 1.5 T for whole-brain histogram analysis and ROI analysis.