Approximately 1/88 children are believed to be affected by Autism Spectrum Disorder (ASD). A more recent study suggests numbers as high as 1/50. With the increased diagnosis of ASD, treatment and understanding of the disorder is a pressing health concern. Protein biomarkers found for ASD may be used for ASD diasgnosis, subtyping, monitoring, treatment, identifying therapeutic targets and may also provide clues about the causes of ASD. Here, sera and saliva samples from children with ASD and matched controls were analyzed using a combination of gel electrophoresis, in gel digestion or in solution digestion and nanoliquid chromatography‐tandem mass spectrometry (nanoLC‐MS/MS) to investigate differences between the proteomes of ASD patients and matched controls. These results will hopefully shed light on possible causes of ASD. In the SDS‐PAGE and Tricine‐PAGE based experiments using sera, increased levels of Apolipoproteins (Apos) ApoA1 and ApoA4, involved in cholesterol metabolism, and of serum paraoxanase/arylsterase 1, involved in preventing oxidative damage, were discovered in the sera of children with ASD, compared with their matched controls. These three proteins are parts of High Density Lipoproteins (HDLs) and are presumed to interact with one another. This data suggests that there may be a dysregulation of cholesterol metabolism in children with ASD. Additional dysregulated proteins were also detected, suggesting a dysregulated immunological response and an enhanced response to environmental toxic factors. This investigation is ongoing.