Metanil yellow is the principal non-permitted food colour used extensively in India. The effects of long-term consumption of metanil yellow on the developing and adult brain were studied using Wistar rats. Regional levels of noradrenaline, dopamine and serotonin, activity of acetylcholine esterase (AChE), and operant conditioning with food reward were assessed in rats fed, metanil yellow and in controls. In the treated rats the amine levels in the hypothalamus, striatum and brain stem were significantly affected, and the changes were not generally reversible even after withdrawal of metanil yellow in developing rats. The striatum showed an early reduction of AChE activity, whereas the hippocampus showed a delayed but persistent effect of reduced AChE activity. Treated rats also took more sessions to learn the operant conditioning behaviour. These effects on these major neurotransmitter systems and on learning, indicate that chronic consumption of metanil yellow can predispose both the developing and the adult central nervous system (CNS) of the rat to neurotoxicity.