The layered alpha-NaFeO₂ structure is one of the most important structural families for battery cathodes.  In recent years, it has been found that a honeycomb-layered superstructure of the basic alpha-NaFeO₂ structure type can produce enhanced specific capacities for Li-ion batteries (Li-excess compounds with Li₂MnO₃ motifs) and enhanced voltages for Na-ion batteries (compounds such as Na₃Ni₂SbO₆ for which the entire discharge capacity is delivered above 3.0 V vs. Na⁺/Na).  However, the crystallography of honeycomb-layered compounds is very complex, which results in the occurrence of both disordered and ordered polymorphs as well as complex long-range c-axis superstructures whose origin has not previously been determined.  New tools for investigating, classifying, and quantifying the disordered in honeycomb-layered compounds have been developed and applied to Na-ion cathode materials with this structure type with an emphasis on the “number” faults associated with the position of the central atom of the honeycomb lattice rather than the “letter” faults associated with the layer position relative to the close-packed atom planes.  This comprehensive work includes Rietveld refinements of synchrotron and neutron diffraction data, pair distribution function analysis, solid state NMR, TEM studies, and complementary electrochemical performance data.  It is demonstrated that there is a continuous spectrum of compositions with varying amounts of number disorder.  This number disorder is distinctly non-random, and the underlying thermodynamic reasons will be discussed, as well as the unusually slow reaction mechanism by which disorder is annealed out of the structure.  Since the structure of honeycomb-layered compounds are strongly dependent on the synthesis history, the methods for quantifying the degree of disorder that will be presented are particularly important if systematic studies on this important class of materials are to be carried out.  It is found that the degree of ordering has a clear impact on electrochemical performance, and thus control over sample disorder is required in order to attain the best cathode electrochemistry.