Morphological, metallographic and structural analyses of aluminium–copper dissimilar welds produced under different friction stir welding conditions were conducted in order to analyse the mechanisms of intermetallic phases formation, its relation with welding conditions and its consequences in the weld structure and morphology. Under lower heat input conditions, only a thin intermetallic layer distributed along the aluminium/copper interface was depicted inside the nugget. Increasing the heat input promoted material mixing and formation of increasing amounts of intermetallic rich structures. The intermetallic phase content and the homogeneity of the mixed area increased with increasing heat input, evolving from structures containing Al, Cu, CuAl₂ and Cu₉Al₄ to structures predominantly composed of Cu₉Al₄ and Cu(Al). In order to explain these results, the mechanisms of intermetallic phases formation are discussed, taking into account the process parameters and material flow mechanisms in friction stir welding. Important relations between intermetallic formation and weld surface morphology were also found.