BALB/cByJ mice have an autosomal recessive deficiency of short-chain acyl-CoA dehydrogenase (SCAD) and show elevated excretion of urinary butyrylglycine, ethylmalonate, and methylsuccinate, which resembles the SCAD deficiency disorder in children. These mice are clinically normal, perhaps because of an efficient acyl-CoA conjugation system. We attempted to decompensate the acyl-CoA metabolism in mutant mice by chronic treatment with a riboflavin-deficient diet for 3 weeks to potentiate the SCAD deficiency. We studied the urinary profiles of organic acids, acylglycines, hepatic and cerebral profiles of carnitines, and ammonia to assess the potentiation of this disorder. Cerebral activity of choline acetyltransferase (ChAT) was determined to study the effects of acyl-CoA accumulation on the cholinergic system. The results indicate that in riboflavin-deficient mutant mice, the excretion of ethylmalonate, methylsuccinate, butyrylglycine, and dicarboxylic acids was enhanced. Hepatic and cerebral free and esterified carnitines were reduced, indicating a potentiation of the secondary carnitine deficiency. Hepatic ammonia levels, but not cerebral ammonia or glutamine levels, were elevated, indicating a tendency towards secondary hyperammonemia. Brain choline acetyltransferase activity was significantly reduced in striatum, implying a reduced availability of cerebral acetyl-CoA or a decreased cerebral transport of choline: Most of these changes were partially or completely restored by a concomitant treatment with acetyl-L-carnitine (ALCAR). In summary, we conclude that BALB/cByJ mice with SCAD deficiency, but with a functional urea cycle, might have an adequate adaptive mechanism to adjust to an excessive acyl-CoA load without hyperammonemia at the cerebral level. However, any deficiency of vitamins or cofactors in the diet could disturb an adaptation to this disorder and produce an effect on the cholinergic system.