Objective: We worked to characterize genetic variants in lipid and sterol related genes in young children affected with autism spectrum disorder (ASD) in an effort to determine the association between lipid and sterol gene sequence variation and neurodevelopmental phenotype. Method: Children with a confirmed ASD diagnosis were recruited from an autism specialty clinic at a regional tertiary academic health center. Participants included 24 children (20 male and 4 female) who were between the ages of 40 to 81 months (M = 60 months).The Autism Diagnostic Observation Schedule and the Merrill-Palmer Scale-Revised were utilized to provide functional neurodevelopmental data. We conducted an exome sequencing workflow to investigate whether novel variants were related to neurodevelopmental severity of ASD. Results: Variants occurred in 355 total genomic positions. Of these variants, 169 were nonsynonymous (31 of which were novel). The total number of variants observed in the exons of captured regions of an individual subject ranged between 88 and 117; novel variants ranged between four and 10 per participant, while nonsynonymous variants ranged between 36 and 51 per participant. The total number of novel variants did not have a significant association with neurodevelopmental severity; however, the total number of nonsynonymous variants per subject was correlated with neurodevelopmental severity. Conclusion: Findings suggests that the amount of nonsynonymous variants lipid and sterol related genes may be a biological marker of how ASD impacts development in the functional areas of cognition, fine motor control, receptive language, memory, speed of processing, and visual motor integration.