When consumed as whole grain, wheat has a high nutrient density that contributes to a healthy diet. Yet, products labeled as whole wheat can still contain a substantial amount of refined grain leading to the confusion for consumers, so a method was designed to determine the whole grain status within wheat-based foods. Wheat germ agglutinin (WGA), a lectin found in the germ tissue of wheat kernels, was evaluated as a biomarker of whole grain wheat. WGA content strongly correlated with the percentage of whole wheat within premade mixtures of whole and refined (white) flours. Then, commercial flours labeled as whole wheat were tested for WGA content and found to contain up to 40% less WGA compared to a whole grain standard. Commercial pasta products labeled as whole wheat were also tested for WGA content and found to contain up to 90% less WGA compared to a whole grain standard. The differences in WGA content were not likely due to varietal differences alone, as the WGA content in common varieties used in domestic wheat flour production varied less than 25%. The levels of other constituents in wheat kernels, including starch, mineral, phytate, and total protein, were not different among the commercial whole wheat flours and pasta products. WGA is a unique biomarker that can identify wheat products with the highest whole grain content. PRACTICAL ABSTRACT: Whole grain wheat has a high nutrient density that can be part of a healthy diet, but products labeled as whole wheat can still contain some refined grain. Wheat germ agglutinin (WGA) was tested as a biomarker to measure whole grain status in wheat-based foods and revealed that some commercial whole wheat flour and pasta contained unexpectedly lower levels of the WGA biomarker compared to a whole grain standard. WGA may therefore be a useful way to test for whole grain wheat content.