Experimentally increasing metabolic flux in a pathway in which an essential step is catalyzed by a vitamin-dependent enzyme (a challenge test) has been used in assessing functional vitamin status and elucidating common and alternate metabolic pathways. Conversion of 3-methylcrotonyl CoA to 3-methylglutaconyl CoA in the leucine catabolic pathway is catalyzed by the biotin-dependent enzyme methylcrotonyl-CoA carboxylase (MCC). Marginal biotin deficiency reduces MCC activity and increases urinary excretion of 3-hydroxyisovaleric acid (3HIA) and 3-hydroxyisovaleryl carnitine (3HIA-carnitine) measured in 24-h urine collections. We assessed urinary excretion of 3HIA and 3HIA-carnitine in response to a leucine challenge in humans made progressively biotin deficient by egg white consumption. In 2 cohorts of healthy adults (Study 1: n = 5; Study 2: n = 7) rendered biotin deficient over 28 d, urinary excretion of 3HIA and 3HIA-carnitine in response to a leucine challenge was quantitated weekly for 3 or 4 wk, respectively. In both studies, mean urinary excretion of both 3HIA and 3HIA-carnitine increased >2-fold by d 14 (P < 0.002 for both indicators for both studies). Diagnostically, both indicators were highly sensitive, but diagnostic sensitivities were not superior to those of 24-h excretion of 3HIA and 3HIA-carnitine. These studies provide evidence that urinary excretions of 3HIA and 3HIA-carnitine in response to an oral leucine challenge are early and sensitive indicators of marginal biotin deficiency in humans. The variability of the proportion of leucine catabolites excreted as 3HIA suggests substantial population heterogeneity in the metabolic capacity of the 3HIA-carnitine detoxification pathway.