Fragile X is the most common single gene cause of autism, responsiblefor 2% to 6% of all cases of autism, Approximately 30% of males withFXS have full autism. Genes known to be causes of ASD interact with thetranslational pathway defective in FXS , and it has been hypothesized thatthere will be substantial overlap in molecular pathways and mechanismsof synaptic dysfunction between FXS and ASD. The present study aimedat detection of molecular and neurobiological similarities between FXSand ASD. Also it aimed at detection of certain metabolic biomarkers thatcould be specific to autism, Fragile X. The present study included 4groups of subjects, 2 diseased groups (20 males patients with Autism and20 males Fragile X syndrome) and 2 control groups (20 Normal healthymales controls and 20 Down Syndrome males patients). The presentstudy concluded that low serotonin levels was exclusively and unique toautistic patients and it can be consider as a metabolic marker for autism.Also we found that autism and FXS share neurobiological similarities asGABA was significantly high in both disorders than normal controlchildren , meanwhile it was specific to Autism and Fragile X Syndromeas GABA level was not high in D.S. On the contrary Down Syndromeshowed lower (non significant) GABA levels than normal healthychildren. Regarding Glutamate, it was high in the 3 disorders but with thehighest levels in Autism followed by Fragile X and Down Syndrome,respectively. The present study didn't find a significant differencebetween autism and controls regarding CGG repeats numbers.