Prefrontal cortical tissue from the Stanley Foundation Neuropathology Consortium, which contains samples from patients with schizophrenia, bipolar disorder, non-psychotic depression, and normal controls (n = 15 per group), was studied in a blinded fashion in 14 different laboratories between 1997 and 2000. The results of 69 separate data sets were analyzed with univariate and multivariate techniques. A total of 17 abnormal markers were identified that pertained to a variety of neural systems and processes, including neuronal plasticity, neurotransmission, signal transduction, inhibitory interneuron function, and glial cells. Schizophrenia was associated with the largest number of abnormalities, many of which were also present in bipolar disorder. Major depression was associated with relatively few abnormalities. The majority of abnormal findings represented a decline in function and could not be easily explained by exposure to psychotropic or illicit drugs. It is argued that the abnormal findings are not simply due to stochastic processes but represent viable markers for independent replication and further study as candidate genes or targets for new treatments.