Introduction: Neurodevelopmental disabilities are common among infants with complex congenital heart disease (CHD). While hemispheric asymmetries in normal fetal brain size and shape have been reported, the effect of CHD on hemispheric development of the developing fetal brain remains unknown. Hypothesis: We hypothesized that emerging cerebral hemispheric asymmetries of the fetal CHD brain would differ compared to healthy controls using in vivo MRI tools. Methods: A total of 252 pregnant women were recruited (164 controls; 88 CHD fetuses), in which 328 fetal MRI scans were performed. Single shot fast spin echo T2-weighted images were acquired on a 1.5T GE MRI scanner. High-resolution 3D models of the fetal brain were reconstructed using slice-to-volume registration method for motion correction and Draw-EM algorithm for automatic segmentation. Volumetric analysis of brain tissues was conducted, and cortical folding measures of brain lobes were evaluated. Mixed effects regression was utilized to compare the brain features between right and left hemispheres for healthy controls and CHD fetuses. Results: The mean gestational age of all fetal MRI studies was 32.1±3.7 weeks (range: 24.0-39.4). For healthy fetuses, the volume of cortical gray matter was higher in the left hemisphere; however, this pattern was diminished in CHD fetuses. Gyrification indices were higher in the parietal and occipital lobes of the right hemisphere for controls, but not for CHD fetuses. Similarly, Gaussian curvature was higher in the right frontal lobe for controls only. Conversely, the surface area of the left occipital lobe was lower in CHD fetuses, but not in healthy fetuses. Conclusions: We report for the first time early disturbances in emerging hemispheric asymmetric patterns of the fetal brain in CHD compared to controls. The extent to which these lateralization differences reflect genetic, epigenetic and/or hemodynamic disturbances in CHD fetuses is under investigation.