Cellulose nanocrystals (CNCs) have high aspect ratios, polydisperse size distributions, and a strong propensity for aggregation, all of which make them a challenging material for detailed size and morphology characterization. A CNC reference material produced by sulfuric acid hydrolysis of softwood pulp was characterized using a combination of dynamic light scattering (DLS), atomic force microscopy (AFM), transmission electron microscopy, and X-ray diffraction. As a starting point, a dispersion protocol using ultrasonication was developed to provide CNC suspensions with reproducible size distributions as assessed by DLS. Tests of various methods for AFM sample preparation demonstrated that spin coating on a positively charged substrate maximizes the number of individual particles for size analysis, while minimizing the presence of agglomerates. The effects of sample-to-sample variability, analyst bias, and sonication on size distributions were assessed by AFM. The latter experiment indicated that dispersion of agglomerates by sonication did not significantly change the size distribution of individual CNCs in suspension. Comparison with TEM data demonstrated that the two microscopy methods provide similar results for CNC length (mean ~ 80 nm); however, the particle width as measured by TEM is approximately twice that of the CNC height (mean 3.5 nm) measured by AFM. The individual crystallite size measured by X-ray diffraction is intermediate between the two values, although closer to the AFM height, possibly indicating that laterally agglomerated CNCs contribute to the TEM width. Overall, this study provides detailed information that can be used to assess the factors that must be considered in measuring CNC size distributions, information that will be useful for benchmarking the performance of different industrially sourced materials.