Background Inability to accurately identify parathyroid glands during cervical endocrine surgery hinders patients from achieving post-operative normocalcemia. An intrinsic near-infrared fluorescence method was developed for real-time parathyroid identification with high accuracy. This study assesses the clinical utility of this approach. Methods Autofluorescence measurements were obtained from 137 patients (264 parathyroid glands) undergoing parathyroidectomy and/or thyroidectomy. Measurements were correlated to disease state, calcium levels, parathyroid hormone (PTH), vitamin D levels, age, sex, ethnicity and body-mass index (BMI). Statistical analysis identified which factors significantly affect parathyroid detection. Results High parathyroid fluorescence was consistently detected and showed wide variability across patients. Near-infrared fluorescence was used to correctly identify 256/264 (97%) of glands. The technique showed high accuracy over a wide variety of disease states, though patients with secondary hyperparathyroidism demonstrated confounding results. Analysis revealed BMI (P<0.01), disease state (P<0.01), vitamin D (P<0.05), and calcium levels (P<0.05) account significantly for variability in signal intensity. Age, gender, PTH, and ethnicity had no effect. Conclusions This intrinsic fluorescence-based intraoperative technique can accurately detect nearly all parathyroid glands in real-time. Its discrimination capacity is largely unlimited by patient variables, but several factors affect signal intensity. These results demonstrate potential clinical utility of optical guidance for parathyroid detection.