Biochemical biomarker studies of ASD individuals have been undertaken in order to identify biochemical alterations that might advance the understanding of the atypical neurodevelopment seen in ASD. In addition, there is the promise that biochemical biomarkers might be useful in predicting risk and in subtyping. Most of the studies to date have examined neurochemical biomarkers related to neural transmission in the central and peripheral nervous systems. We first deal with neurochemical studies measuring levels of neurotransmitters, their metabolites, and associated enzymes in blood, urine, and cerebrospinal fluid (CSF). Separate sections cover serotonin, dopamine, and stress response systems (including the central noradrenergic, sympathoadrenomedullary, and hypothalamic‐pituitary‐adrenal axis systems). Following sections review research on melatonin, sex hormones, neuropeptides including oxytocin, amino acids and acetylcholine, purines and related compounds, immune‐related measures, oxidative stress/redox status, and “omics” research.