During growth and post-harvest storage, fungi can infect grain and produce secondary metabolites known as “mycotoxins ”. Some mycotoxins are regulated due to their potential hazardous health effects. Thusly, analysis of bulk grain consignments for mycotoxins is common in the grain trade. The heterogeneity of bulk grain with respect to deoxynivalenol (DON) and ochratoxin A (OTA), two regulated mycotoxins, was investigated. Variation of concentrations amongst individual wheat kernels was assessed, along with the variation within sub-samples and test portions produced from 10 kg laboratory samples, and amongst 500 t increments sampled during loading of bulk shipments (4,600 to 55,000 t). Concentrations in individual kernels ranged from < 0.02 to 583 mg/kg for OTA and < 0.3 to 414 mg/kg for DON. Analysis of the distribution of concentrations was limited due to the difference between the sample sets available for use; one was naturally infected (DON) and the other was inoculated and incubated under laboratory conditions (OTA). Bulk shipments were sampled during loading using a Canadian Grain Commission-approved automated cross-stream diverter-type sampler and in-line divider. Increments were combined, and 10 kg laboratory samples were prepared from the resulting composite using a Boerner divider, comminuted using a rotor beater mill, and sub-sampled using rotary sample division to produce representative sub-samples and test portions. Concentrations of OTA in the 500 t increment samples varied from < 0.25 to 22.9 µg/kg; DON varied from < 0.05 to 0.67 mg/kg. Within shipments, the OTA concentrations varied more amongst increments than did DON. The coefficients of variation for OTA ranged from 42 to 95% which were 2-4× greater than for DON. The results illustrate heterogeneity of bulk wheat relevant to international trade and regulated mycotoxins. Differences observed for DON and OTA also reflect how biological differences in mycotoxin production contributes to the challenges faced in analysing bulk whole grain for mycotoxins.