Regional brain levels of serotonin (5-HT), 5-hydroxyindoleacetic acid (5-HIAA), dopamine (DA) and norepinephrine (NE) were determined in alcohol-naive rats from lines selectively bred for alcohol preference (P) and alcohol aversion (nonpreference, NP). Based on comparison by a standard t-test, the P rats had 12% lower NE in the pons-medulla, 20% higher NE and 16% lower DA content in the cerebral cortex (CX) than did the NP rats. However, the predominant finding was that the levels of 5-HT and 5-HIAA were 12-26% lower for the P than for the NP rats in the CX, hippocampus (HIP), corpus striatum (STR), thalamus (TH) and hypothalamus (HY). Regional CNS monoamines from a group of independently bred, stock Wistar rats were also compared with the NP and P groups to determine if the selectively bred rats differed widely from an unselected population. In most instances, the NP and P rats fell within the range of the stock group. When the stock group was included in an analysis of variance of the data, post-hoc differences between the NP and P groups that remained significant were the lower levels of 5-HT (and in some cases 5-HIAA) in the CX, HIP, STR, TH and HY of the P group. In the HY and HIP, the 5-HT levels of the P and NP animals diverged significantly in opposite directions from those of the stock group, possibly suggesting an involvement of these regional serotonergic systems in alcohol preference.