A comparison was made between dry milling and slurry mixing as comminution step preceding mycotoxins analysis. Such in respect to EC legislation that consists of sample schemes up to 30 kg. Cacao, green coffee, almonds and pistachio samples of 10 kg were milled by a RAS mill and all three sub-samples were completely analysed for aflatoxin B1 or Ochratoxin A. The differences in analytical results are explained by measurements of particle size distributions of both milling types. The obtained data are compared with literature data on coefficients of variation (CV) for various milling procedures. For dry milling CV values were generally not below 20 % for aflatoxin B1 levels up to 38 µg/kg in peanuts, whereas slurry mixing could achieve CV values below 5 % at aflatoxin B1 levels down to 4 µg/kg in pistachios. Measurements also showed possible difference in mycotoxin content of a sample between both milling types. This could lead to false positive or negative results when rejecting or accepting a lot, as this is based on the sample result. It was concluded that slurries contain smaller particles than dry milled samples and thus generate the lowest possible CV values which in turn leads to better sample homogenisation.