Prenatal exposure to alcohol can have a serious impact on the development of an embryo/fetus and affect subsequent cognitive and neural development. The current study aimed to explore 1) whether children with heavy prenatal alcohol exposure exhibit inattention and hyperactivity as compared to the controls; 2) whether there were morphometric differences between groups in the prefrontal cortex and cerebellum; 3) whether prefrontal cortex structure was associated with inattention, and whether cerebellum structure was related to hyperactivity. The current study was a retrospective analysis on subjects with heavy prenatal alcohol exposure (AE) or no/minimal exposure (CON) who were previously recruited as part of a larger study at the Center for Behavioral Teratology at San Diego State University. A hundred and eleven children participated in the behavioral task (AE: n = 48; CON: n = 63) and, of these, 47 children participated in the magnetic resonance imaging (MRI) portion of the study (AE: n = 24; CON: n = 23). Performance on an attention task and movement was measured via the Quotient ADHD System. A high-resolution T1-weighted anatomical scan was acquired for each participant using a General Electric (GE) Discovery MR750 3.0 T scanner and was processed using FreeSurfer v6.0. Regions of interest (ROI) included prefrontal cortex and the cerebellum. Outcome measures extracted included surface area, cortical thickness and volume for the prefrontal cortex and volume for the cerebellum. The AE group made more omission errors and had more variability in response time than the CON group but did not significantly differ from the CON group on any measures of movement. The AE group had smaller prefrontal cortex and cerebellum volume than the CON group. Prefrontal cortex surface area and cortical thickness did not differ between AE and CON groups. Regression analysis did not show significant associations between prenatal alcohol exposure, prefrontal cortex and cerebellum, and attention and movement. This study supports that prenatal alcohol exposure impacts attention and the structure of the prefrontal cortex and cerebellum, although the association between brain structure, attention deficits, and movement in children with prenatal alcohol exposure remains inconclusive.