A variety of models have been suggested for the cross-sectional shape and dimensions of cellulose nanocrystals (CNCs). Although many studies report measurements of CNC width (from transmission electron microscopy, TEM) and height (from atomic force microscopy, AFM), few have measured both cross-sectional dimensions for the same CNC sample and the same particles. Previous work has demonstrated that the TEM width is approximately twice the AFM height, a result that was explained by lateral aggregation of CNCs. Here we examine this question in more detail by measuring both CNC width and height by a single technique, AFM. The ability to measure both cross-sectional dimensions was facilitated by several factors: access to a fractionated CNC sample with few agglomerated particles, AFM imaging at low applied force with a small, nominal probe radius and in situ calibration of the AFM probe radius using co-deposited gold nanoparticles (AuNPs). Two sizes of AuNPs provided optimal calibration of the tip radius and allowed internal validation of the approach. The results show that the CNC width/height ratio covers a relatively wide range with a larger variation in width than height. The ratios indicate that approximately a third of the particles adsorb with their shorter cross-sectional side on the surface. A fraction of CNCs (28%) have an approximately symmetric cross-section whereas the remainder are asymmetric with one axis that is 2–3 times longer than the other. The results are consistent with a combination of laterally aggregated CNCs that cannot be resolved as individual particles and CNC particles that are comprised of multiple crystallites. This has important implications for applications in which the particle length/cross-section determines the CNC properties.