Cellulose nanocrystals (CNCs) were analyzed by asymmetric flow field-flow fractionation (AF4) coupled with multiangle light scattering (MALS) detection. Small fractions were collected from the output of the AF4 apparatus for investigation by transmission electron microscopy (TEM). The influence of CNC injection amount, the number of passes through a high-pressure homogenizer, and different CNC sources on the elution behavior and particle size distribution was investigated. The AF4-MALS results on crystal length were compared with those from TEM. Peak distortion and variation in elution profiles with the increase in sample load were observed. Good resolution was obtained when the injection mass varied from 20 to 40 μg, corresponding to injections of 4-8 μL at a starting concentration of ~5 μg/μL; concentrations during the separation process and at the detector were significantly lower. As the number of homogenization treatments increased, the peak shape became narrower and more symmetrical. This indicates a narrowed crystal length distribution, but regardless of source or homogenization treatment, no CNC preparation was as uniform as tobacco mosaic virus, a well-known rigid rod model structure, whose length was found by AF4-MALS to be in agreement with literature values. CNCs derived from cotton contained longer crystals than those derived from microcrystalline cellulose, as shown by both AF4-MALS and TEM techniques. An advantage of AF4-MALS compared to TEM is the ability to sample large numbers of rodlike particles, which is challenging and time-consuming for TEM image analysis, especially without the presorting afforded by AF4. The good TMV results suggest a high degree of accuracy will pertain to the CNC size distribution measurements.