This study was undertaken to test two assumptions critical for use of [2-C-14]acetate to measure gluconeogenesis in vivo. For the assumption that incorporation into glucose of products of [C-14]acetate metabolism does not affect the distribution of label within the glucose molecule, we infused [2-C-14]acetate in 17 healthy subjects and [3-C-14]lactate in 10 healthy subjects and compared the ratio of the resultant specific activities of plasma glucose carbons 1, 2, 5, 6, and 3, 4 obtained with each tracer. The ratio obtained with [2-C-14]acetate (2.99 +/- 0.07) was significantly different from the ratio obtained with [3-C-14]lactate, (3.82 +/- 0.2, P < 0.01). Because the model predicts that these ratios should be identical, these results indicate that either the model is incorrect or that metabolism of [C-14]acetate to other compounds affects the distribution of the label within the glucose molecule. To test the assumption that plasma 3-OH-butyrate specific activity approximates the specific activity of hepatic intramitochondrial acetyl CoA, we compared the ratio of specific activities of plasma glucose and 3-OH-butyrate obtained in 7 healthy subjects infused with [2-C-14]acetate and [2-C-14] octanoate. The ratio obtained with [2-C-14]acetate (0.18 +/- 0.03) was significantly different from that obtained with [2-C-14]octanoate, (0.10 +/- 0.02), P < 0.001. These results suggest compartmentalization of acetyl CoA within liver mitochondria and indicate that plasma 3-OH-butyrate specific activity may not necessarily approximate intramitochondrial acetyl CoA specific activity during [2-C-14]acetate infusion. We conclude that assumptions critical for use of [2-C-14]acetate to measure gluconeogenesis in vivo are not valid.