The experimental findings that the quark masses and mixing angles in the Standard Model are so much different is considered to be unnatural because they originate from a single mechanism - the Higgs mechanism. This is known as the quark flavour puzzle and in this thesis we discuss two approaches to resolve it. Incorporating the concept of minimal flavour violation, we promote the Yukawa entries to dynamical spurion fields in an effective field theory. Their vacuum expectation values sequentially break the maximal flavour symmetry of the Standard Model and generate the hierarchy of the quark masses and mixing angles. In Randall-Sundrum models the five-dimensional quark mass matrices render the effective four-dimensional Yukawa matrices hierarchical by a different quark localisation in the extra dimension. In both models we focus on possible flavour-changing neutral currents that are constrained by experiment.