Deficiency of biotin at the tissue level can be assessed indirectly by measuring the urinary excretion of 3‐hydroxyisovaleric acid. This paper describes the application of an improved method of quantifying urinary 3‐hydroxyisovaleric acid using unlabeled and uniformly deuterated 3‐hydroxyisovaleric acid. These compounds were synthesized by a modification of the lithioacetic acid method for generation of beta‐hydroxy acids. Elemental analysis, nuclear magnetic resonance, gas chromatographic and gas chromatographic/mass spectrometric data demonstrated that the compounds are greater than 95% pure. Mass spectrometry confirmed the identity of the unlabeled compound, demonstrated that the deuterated compound is uniformly labeled, and offered insight into the pattern of mass fragmentation. The method for determination of the concentration of 3‐hydroxyisovaleric acid in rat urine uses gas chromatographic/mass spectrometric quantification of the di‐trimethylsilyl derivative with the deuterated compound as the internal standard. Results provide evidence that this method is more accurate than a previously published method that did not utilize the unlabeled and deuterated standards.