By differential scanning calorimetry (DSC), the effect of thermal treatments on the melting of tetrafluoroethylene-perfluoroalkylvinylether copolymers (PFA) with different contents of perfluoromethylvinylether as a comonomer has been investigated. Two melting peaks can be identified for all copolymers, whose presence, value, and extent depend upon the thermal treatments. The higher temperature one, scarcely influenced by the crystallization conditions (i.e., cooling rate and annealing), can be attributed to more perfect crystals present in the original samples. The lower temperature one is produced only by annealing (annealing peak) and can be interpreted as resulting from much poorer crystals grown among the larger ones. For the copolymer with the lowest content of comonomer, the effect of thermal treatments on the low-temperature (crystal-crystal) transitions has also been studied. The rejection of the counits from the crystals, at least in equilibrium conditions, is confirmed.