Juniper (Juniperus spp.) foliage is consumed by free-ranging goats in the southwestern US. Junipers contain monoterpenes which have toxicological and pharmacological effects. We sampled 20 male Spanish goats (Capra hircus; 10 young [2-year-old] and 10 old [3-5-year-old]) from a herd selected for their propensity to consume a high (estimated breeding value [EBV] = 13.01 ± 0.20) or low (EBV = -14.76 ± 0.48) proportion of juniper in the diet to determine the ability of near infrared spectroscopy (NIRS) in detecting physico-chemical differences in animal tissues. Heart (ventricle; interior and exterior surfaces), liver (caudate lobe), and muscle (longissimus dorsi) samples as well as an entire kidney and testicle, were collected at harvest (n = 5 of each age [i.e. length of exposure to monoterpenes] and juniper EBV combination). Tissue samples were stored in whirl-pac bags at -20o C and later thawed to ~24o C for NIRS analysis. Spectra (400–2500 nm) were obtained with an ASD Field Spec using a contact probe directly through the whirl-pac sample bag. Principal component and partial least squares regression procedures were accomplished in SAS; P > 0.05 indicated statistical significance. Both age (RSQ, 0.2 to 0.6; P > 0.05) and juniper EBV (RSQ, 0.2 to 0.65; P > 0.05) were correlated with near infrared (NIR) spectral characteristics. Propensity to consume juniper was most strongly correlated with NIR spectra in testicular tissue (RSQ = 0.65, MSE = 0.25, P > 0.01), and least strongly correlated in the heart interior surface (RSQ = 0.21, MSE = 0.21, P > 0.05). Spectral correlations with propensity to consume juniper were stronger in tissues from old (RSQ ~ 0.68) than young (RSQ ~ 0.52) goats, especially in liver, kidney, muscle, and testicle. Physico-chemical differences in goat tissues were affected by genetic propensity to consume juniper, and these were detected by NIRS.