We conduct a general discussion of supersymmetric models with three families in the Higgs sector. We analyse the scalar potential, and investigate the minima conditions, deriving the mass matrices for the scalar, pseudoscalar and charged states. Depending on the Yukawa couplings and the Higgs spectrum, the model might allow the occurrence of potentially dangerous flavour changing neutral currents at the tree-level. We compute model-independent contributions for several observables, and as an example we apply this general analysis to a specific model of quark-Higgs interactions, discussing how compatibility with current experimental data constrains the Higgs sector.

30 pages, 9 figures. Comments and references added. Final version published in Physical Review D