Soybean physical and chemical properties changed by size (from 4.8 to 8.8 mm diameter), but soybean size and seed density did not affect the protein and oil determination accuracy of three near-infrared transmission analyzers. Corn samples were also separated by size and kernel density. Changes in corn kernel density and size introduced small errors in near-infrared transmission protein, oil, and starch measurements. In corn protein, the maximum error was about ±0.2% points. A robust calibration set is needed to eliminate the weak seed weight and density effects, as well as to support the corn density calibration for near-infrared analyzers.