Fusarium infected grain is separated by comparing reflected and transmitted light at two wavelengths, one at which the light is substantially reflected and scattered the same by healthy and infected kernels, the other at which the light is reflected and scattered to a significantly greater degree by infected than healthy kernels. An apparatus having a rotating apertured cylinder, with a low internal vacuum, allows comparison of individual kernels. When comparison indicates that a kernel is infected, a lever dislodges it from the cylinder allowing it to fall into a receptacle for infected kernels. Kernels remaining on the cylinder are scraped off to fall into a receptacle for healthy kernels. Although results vary, to some extent depending on the degree of infection, approximately 90% of healthy kernels and 5% of infected kernels are deemed “healthy”, while approximately 10% of healthy kernels and 95% of infected kernels are deemed “infected,” reducing the level of infected kernels.