Carbonate-intercalated layered double hydroxides of Co(II) and Ni(II) with Fe(III) and Al(III) were precipitated under different conditions (pH = 8–12; T = 25–80°C). All the samples are replete with stacking faults which are not eliminated by post-precipitation hydrothermal treatment (80–180°C, 18 h). DIFFaX simulations show that the layer stacking sequence of the disordered samples can be generated by a mixture of motifs corresponding to the 3R1 and 2H1 polytypes. These specific sequences are selected in preference to others because of the need for hydrogen bonding between the intercalated carbonates and hydroxide sheets. Thermodynamic considerations show that faulted crystals have greater stability than ordered crystals. Stacking faults arising from a mixture of 3R1 and 2H1 motifs, while having the same enthalpy as that of the ordered crystal, nevertheless contribute to thermodynamic stability by enhancing disorder.