Abstract Biomarkers promise biomolecular explanations as well as reliable diagnostics, stratification, and treatment strategies that have the potential to help mitigate the effects of disorders. While no reliable biomarker has yet been found for autism spectrum disorder (ASD), fatty acids have been investigated as potential biomarkers because of their association with brain development and neural functions. However, the ability of fatty acids to classify individuals with ASD from age/gender-matched neurotypical (NEU) peers has largely been ignored in favor of investigating population-level differences. Contrary to existing work, this classification task between ASD and NEU cohorts is the main focus of this work. The data presented herein suggest that fatty acids do not allow for classification at the individual level.