The evolution equations of the Yukawa couplings and quark mixings are performed for the one-loop renormalisation group equations in six-dimensional models compactified in different possible ways to yield standard four space-time dimensions. Different possibilities for the matter fields are discussed, that is where they are in the bulk or localised to the brane. These two possibilities give rise to quite similar behaviours when studying the evolution of the Yukawa couplings and mass ratios. We find that for both scenarios, valid up to the unification scale, significant corrections are observed.