Correlated atomic-force and fluorescence microscopy are used to study single-particle versus ensemble fluorescence quantum yields (QY) of semiconductor nanocrystals by measuring a simultaneous map of the topography and the single-particle fluorescence. CdSe/ZnS nanocrystal quantum dots and quantum rods with high QY were investigated. A significant portion of dark particles is detected. Comparison with the ensemble solution QY shows that samples with higher QY have a larger fraction of bright particles accompanied by an increased single-particle QY. Saturated emission from single nanocrystals could not be detected because of particle darkening under high-power excitation.