Near-infrared spectroscopy (NIRS) was used to detect scab damage and estimate deoxynivalenol (DON) and ergosterol levels in single wheat kernels. Results showed that all scab-damaged kernels identified by official inspectors were correctly identified by NIRS. In addition, this system identified more kernels with DON than did a visual inspection. DON and ergosterol were predicted with standard errors of approximate to 40 and 100 ppm, respectively. All samples with visible scab had single kernels with DON levels >120 ppm, and some kernels contained >700 ppm of DON. This technology may provide a means of rapidly screening samples for potential food safety and quality problems related to scab damage.