Magnetic resonance imaging (MRI) studies have shown smaller volumes of grey matter (GM) and white matter (WM) both in schizophrenia and among patients with alcohol abuse or dependence. The effect of alcohol consumption in non-clinical alcohol consumers, i.e. subjects not recruited as having alcohol use disorders is less studied. In the present study, we investigated the effects of alcohol consumption, antipsychotic medication and a diagnosis of schizophrenia on variation in brain volumes among patients recruited for having schizophrenia and a group of age and gender matched control subjects. A total of 69 patients with schizophrenia (n=56), schizoaffective disorder (n=12) and schizophreniform disorder (n=1) and 97 control subjects were included. Alcohol Use Disorder Identification Test (AUDIT) was used to estimate alcohol consumption. In the entire group of patients and controls higher AUDIT score was significantly related to smaller volumes of WM. When ten patients and six control subjects who met lifetime diagnostic criteria for alcohol use disorders were excluded only a trend level association between AUDIT score and WM volumes was found. Having a diagnosis of schizophrenia was related to smaller volumes of total, frontal and temporal WM, total and temporal GM, and larger volumes of total, frontal and temporal cerebrospinal fluid (CSF). A diagnosis of schizophrenia remained a significant factor for smaller WM volumes even when the effect of alcohol consumption was taken into account. Antipsychotic medication was related to larger volumes of temporal CSF. This study demonstrates that alcohol consumption is an important factor for variation in WM volumes, and this effect should be taken into account in all studies evaluating brain volumes from MR images.