In this paper, we describe results from a preliminary experiment on the development of a near infrared reflectance (NIR) calibration for single kernel (SK) % protein content in barley. The SKNIR calibration was developed using kernels from breeding lines and commercial barley varieties with a range in protein content of 7.3% to 16.6% "as is" . The calibration model produced an R 2 = 0.903, while the validation set had a R 2 = 0.837 with a standard error of cross validation and a standard error of prediction of 0.8% for both the calibration and validation sets respectively. The calibration was then used to estimate the variation in % protein of 4,000 single kernels from a commercial variety (Gairdner at 9.3% protein) by segregating kernels into six sub-groups (<7.8%, 7.9-8.3%, 8.4-9.0%, 9.1-9.7%, 9.8-10.4%, >10.5% "as is" ). These sub-groups then had additional grain quality tests carried out including grain size, thousand kernel weight and NIR estimates of % protein, starch, hardness and barley hot water extract (HWE). The results showed an increase in grain size, and a decrease in HWE from the low to high % protein sub-groups. While only a single variety was used in the SKNIR protein segregation study, the results suggested SKNIR could be used to screen for the variation in grain quality traits based on variation in protein content.