Cellulose nanocrystals (CNCs) were prepared from kraft pulps of eucalyptus, birch, and softwood. The different kraft pulps were hydrolyzed using strong sulfuric acid in order to obtain colloidally stable CNCs. The CNCs were studied using flow cytometry (FCM). The light scattering properties of the CNCs in side direction and forward direction were documented. The use of a selective staining agent in combination with FCM analysis enabled detection of the hydrophobic particle populations within the CNC suspensions. The hydrophobic particles were seen clearly in the CNCs from the eucalyptus and birch kraft pulps, but not in the CNCs from softwood pulp. These particles were shown to be linked with the content of lipophilic extractives, especially sterols, present in the kraft pulps. From this fact, it was concluded that FCM analyses offer useful information about the properties of CNCs in suspension. It was also concluded that the content of lipophilic extractives in different raw materials should be determined and considered prior to CNC production. Pre-extraction steps might be needed in order to produce high-quality CNCs from various raw materials, even from kraft pulps.