Aims: To investigate whether the duration of chronic pain in temporomandibular disorder (TMD) patients is associated with a net depletion of amino acids, and a distinct process from pain intensity. Methods: Twenty-nine patients defined by the research diagnostic criteria/TMD as having Type 1a muscle pain (TMD1A group), and 34 age- and sex-matched control subjects, were assessed for variation in urinary organic and amino acid excretion by gas chromatography-mass spectrometry. Results: The TMD1A patients' mean pain intensity, assessed on a visual analog scale (VAS), was 5.4 (95% confidence limits: 4.5 to 6.3), TMD1A illness duration was 5.0 ± 1.2 (SD) years, number of body areas with pain/subject was 6.3 ± 2.4 (range 0 to 10), and symptom prevalence from the Symptom Check List-90-Revised (SCL-90-R) was 25.5 ± 11.3 symptoms/subject, which was higher than the controls (5.2 ± 5.0 symptoms/subject, P .001). TMD1A patient illness duration was positively correlated with symptom prevalence and body pain distribution, and all were independent of pain intensity. The TMD1A patients had: (1) an increased tyrosine:leucine ratio; and (2) reduced leucine concentrations (both P .001), which suggests deregulated catabolism. Pain intensity was associated with: (1) changes in the multivariate urinary metabolite excretion patterns (P .001); (2) reduced leucine concentrations (P .001); and (3) increases in total urinary metabolites (P .04), and in 2 unidentified molecules, UM28 (P .001) and CFSUM1 (P .002). TMD1A illness duration was associated with lower (1) urinary metabolite concentrations and (2) succinic acid and combined glutamine + glutamic acid levels, suggesting a progressive depletion of metabolite reserves. Conclusion: In TMD1A patients, total amino acid excretion was positively correlated with pain intensity and negatively correlated with illness duration, which indicated that illness duration was associated with a different set of metabolic anomalies compared with those identified for pain intensity. Keywords: pain, facial pain, fibromyalgia syndrome, temporomandibular joint dysfunction