Encapsulation of materials into capsules becomes discrete at small scales. We propose a measurement and analysis method of discrete encapsulation of nanomaterials in colloidal capsules, with the volume of fL to pL, using the fluorescence flow cytometry. Encapsulation of nano-sized polymer beads and lambda-phage DNA into lipid vesicles (liposomes) is evaluated as a model system. By using fluorescence markers, vesicle volume, membrane quantity and nanomaterials in a large number of individual vesicles are measured simultaneously. We show that the number of encapsulated material (k = 0, 1, 2, …) can be evaluated from the quantized fluorescence intensity distribution, which is then compared with the Poisson statistics. As a result, probability of encapsulating beads and λDNA exhibits characteristic trends that depend on the vesicle volume, lamellarity, and electrostatic interaction, which should reflect the physical interaction in the vesicle formation processes. This measurement and analysis will be a powerful tool in designing the colloidal capsules used in many scientific and industrial applications.