The septal region, including the cavum septi pellucidi (CSP), and the fornix are part of the limbic system. The majority of MRI- and postmortem studies indicate that enlarged CSP are implicated in the pathology of schizophrenia, but the majority of MRI-studies show that enlarged CSP are not involved in the pathology of bipolar and major depressive disorders. The MRI and post-mortem studies on the role of the fornix in schizophrenia point to a discrepancy in the results. Our review of the role of the CSP in schizophrenia and affective disorders summarizes 29 studies and one meta-analysis. Furthermore, our review of the involvement of the fornix in schizophrenia and affective disorders evaluates 14 studies and one meta-analysis. The discrepancies in the results of the CSP and the fornix might be explained by differences in the methods and sample sizes as well by publication bias.