Objective To explore the levels of sphingolipid metabolites in serum and their relations with clinical diagnosis scale and evaluate their clinical diagnostic values of autism. Methods 73 cases of children with autism and 63 normal control children were selected and determine sphingolipid metabolites levels in the serum of autistic children.Another 100 autistic children and 100 normal control children were selected to determine the levels of sphingolipid metabolites further and analyzed their correlations with the scores of Autism Behavior Checklist ABC and Childhood Autism Rating Scale (CARS), then drew their receiver operating characteristic (ROC) curves. Results Two sphingolipid metabolites, phytosphingosine (PSO) and sphingosine-1-phosphate (S1P), were found to be potentially associated with autism, both of them had significant increases in the serum levels of autistic children than those of normal group.The serum levels of both metabolites were obvious higher of autism in validation group, too.There was positively correlation between the levels of S1P and the scores of ABC.Both area under curve (AUC) and maximum of Youden index of PSO were 1.000, respectively and the best cut off value was 44.883.Sensitivity and specificity was 100% respectively.Both AUC and maximum of Youden index of S1P were 0.961 and 0.868.The best cut off value was 47.678.Sensitivity was 91.7% and specificity was 95.1%. Conclusions There are significant differences between two groups for the serum levels of PSO and S1P.The metabolic abnormality of sphingolipid metabolism may have a potential correlation with autism.Both the PSO and S1P had potential diagnosis values for autism and the best cut off values are 44.883 and 47.678.