Near infrared spectroscopy technique is widely used to nondestructively inspect agricultural products. The Monte Carlo method was used to simulate light propagation in onion bulbs. The measurement system using fiber probes was modeled. The detected diffuse reflectance signals were calculated and the effects of dry skins on the measurements were analyzed. The results showed that the dry skin reduced the signal strength detected, but had little influence on the average penetration depth. At the wavelength of 800 nm, a sourcedetector separation between 0.9 and 2.0 cm is preferred to reach an average penetration depth of 0.5 to 0.8 cm and is capable of detecting the neck rotinfected flesh located in this depth. Using fiber probes with lager acceptance radii and numerical apertures helps increase the measurement sensitivity.