Objective: Chronic fatigue syndrome (CFS) is an illness defined by unexplained disabling fatigue lasting longer than six months, together with at least four out of eight specified symptoms. The etiology and pathophysiology of CFS are to a large degree unknown. Since much remains unclear about CFS we wanted to investigate transcript expression levels in peripheral blood mononuclear cells to identify genes that are involved in CFS. Method: Transcript expression profiles for 20 CFS patients were compared with 14 healthy controls using microarray technology. Results were verified with real-time PCR. Results: We have identified significantly differentially expressed genes comparing a female CFS patient subgroup with gradual illness onset and no previously documented infection with female healthy controls. We have also created a list of genes with indicated, but not verified, expression differences from comparisons between other subgroups and healthy controls. These genes are candidates for further study of potential involvement in CFS. Conclusion: Our results stress the necessity of subgrouping the heterogeneous CFS patient cohort. The mRNA expression differences identified here may be causal factors for the illness or symptoms observed in these patients, or a result of altered functions of other cellular components involved in the illness. The role of these genes in the CFS pathology needs further investigation.