A study was conducted to determine the distribution of deoxynivalenol (DON) and ochratoxin A (OTA) in a lot of 261 of wheat kernels. Within this study, two different sampling and sample preparation strategies were carried out. On the one hand, following the official commission regulation 401/2006/EC, an aggregate sample out of 100 incremental samples was build, homogenized and prepared for laboratory analysis. On the other hand each individual subsample was investigated for its deoxynivalenol and ochratoxin A content. The determined concentration of DON in the individual samples was in a range from 830 up to 2655 (μg/kg, for OTA results ranged from < 0.2 up to 8.6 μg/kg. Thus, a coefficient of variance of 25% for DON and 200% for OTA was achieved. From this, a spot formation for OTA was observed and the average value of the 100 incremental samples did not correspond to the achieved value for the aggregate sample. While the DON contamination at this concentration range seems to be more even, consequently the result of the aggregate sample was in accordance with the average value.In addition a sample communition study was performed to answer the question whether the time consuming process of grinding of the whole aggregate sample is necessary or not. The results of this study show that contamination of whole wheat kernels with DON is at the same level within a 1 kg sample (CV 16%), while OTA contamination shows high variability (CV 94%). At least for OTA this study indicated that an extensive and complete sample communition of the high volume aggregate sample is necessary.