Cannabis consumption is a well known risk factor for the onset of schizophrenia and evidence accumulates that the endocannabinoid system may play a central role in the disease etiology. Using a clinical bioinformatics approach, we have previously found primary fatty acid amides, which are linked to the endocannabinoid system, to be elevated in drug naive schizophrenia and affective disorder. Here, we provide a detailed description of these findings and expand the investigation by analyzing serum from 74 patients after short term treatment with antipsychotic medication using a liquid chromatography-mass spectrometry (LC-MS) metabolomics approach. We show that primary fatty acid amide (pFAA) levels normalize after treatment with typical but not after treatment with atypical antipsychotic medication. Also, the comparison of pFAA levels in schizophrenia patients to those of sleep deprived healthy volunteers suggests that pFAA abnormalities were not related to changes in the sleep architecture of patients with mental illness. Our findings support the involvement of the endocannabinoid system in the pathology of schizophrenia.