Rats were fed for an 8-week period a low riboflavin diet(5ug riboflavin/day) or a control diet(30ug/day) supplied either ad libitum or by pair feeding in order to study the effect of riboflavin on the metabolism of lipids and neurotransmitters. Erythrocyte glutathione reductase (EGR) and monomine oxidase(MAO) activity in the liver and brain were assayed. EGR activity coefficient in riboflavin deficient rats was significantly higher than in ad libitum controls whereas MAO activity was decreased in the deficient rats. Fatty acid composition showed a different trend in the serum, liver and brain. In the serum, the concentrations of essential fatty acids and $omega$-3 fatty acids(eicosapentaenoic acid, docosahexaenoic acid)were decreased about 20-40% in the deficient and pair-fed than in the ad libitum controls. Brain serotonin and 5-HIAA(5-hydroxyindole acetic acid) concentrations were decreased in the riboflavin deficient rats. Learning ability measured by a water maze and exploratory activity using the open field test were not impaired in the deficient rats. These results indicate that brain lipid metabolism was protected in subclinical riboflavin deficiency, however, riboflavin deficiency affected brain serotonin content.