•Sex influenced the extent to differences in mRNAs in lymphocytes (PBLs) between schizophrenics (CSZ) and controls (NPC). There were differences between in CSZ vs NPC among males but not females.•In PBLs of males DNMT1 and DMNT3A mRNAs in of CSZ were higher in than in NPC. This corresponded to higher levels of DNMT1 in the post mortem brain samples of CSZ.•Although GABAergic GAD67 mRNA was lower in post-mortem brain samples of CSZ vs NPC, in PBLs GABAergic mRNAs were higher in CSZ than NPC.•Treatment with clozapine significantly affected the levels of several mRNAs in PBLs of CSZ and treatment with clozapine explained most of the difference in mRNAs between CSZ vs NPC in these mRNAs. Some of the biochemical abnormalities underlying schizophrenia, involve differences in methylation and methylating enzymes, as well as other related target genes. We present results of a study of differences in mRNA expression in peripheral blood lymphocytes (PBLs) and post-mortem brains of chronic schizophrenics (CSZ) and non-psychotic controls (NPC), emphasizing the differential effects of sex and antipsychotic drug treatment on mRNA findings. We studied mRNA expression in lymphocytes of 61 CSZ and 49 NPC subjects using qPCR assays with TaqMan probes to assess levels of DNMT, TET, GABAergic, NR3C1, BDNF mRNAs, and several additional targets identified in a recent RNA sequence analysis. In parallel we studied DNMT1 and GAD67 in samples of brain tissues from 19 CSZ, 26 NPC. In PBLs DNMT1 and DNMT3A mRNA levels were significantly higher in male CSZ vs NPC No significant differences were detected in females. The GAD1, NR3C1 and CNTNAP2 mRNA levels were significantly higher in CSZ than NPC. In CSZ patients treated with clozapine, GAD-1 related, CNTNAP2, and IMPA2 mRNAs were significantly higher than in CSZ subjects not treated with clozapine. Differences between CSZ vs NPC in these mRNAs was primarily attributable to the clozapine treatment. In the brain samples, DNMT1 was significantly higher and GAD67 was significantly lower in CSZ than in NPC, but there were no significant sex differences in diagnostic effects. These findings highlight the importance of considering sex and drug treatment effects in assessing the substantive significance of differences in mRNAs between CSZ and NPC.