During the melt-extrusion of blends of aliphatic polyamide 46 (PA 46) and aromatic polyamide 61 (PA 61), transamidation reactions occur between the blend components. This yields polyamide copolymers consisting of crystallisable PA 46 and noncrystallisable PA 61 sequences. The effect of the copolymer formation on the semicrystalline morphology is studied by time-resolved SAXS and WAXS measurements using synchrotron radiation and by transmission electron microscopy. From WAXS patterns it is noticed that only an excess of PA 61 in the blends affects the PA 46 crystal unit cell at room temperature by hindering or inhibiting the Brill-transition during cooling from the melt. Close to the melting or crystallisation point, the PA 46 crystal structure is independent of the blend composition or thermal history. Consequently, the observed melting point depression cannot be ascribed to less perfect PA 46 crystals, but to a smaller lamellar thickness of the crystallised PA 46 sequences which is confirmed by TEM.