Grazing incidence small-angle X-ray scattering (GISAXS) is used for nondestructive characterization of colloidal crystals of different numbers of hexagonally dense packed layers fabricated by convective self-assembly. Whereas small crystallites with random orientation were obtained in case of monolayers, the scattering data obtained from multilayer samples revealed colloidal domains over areas of a few centimeters where the single crystalline domains are mainly aligned along the growth direction. The data indicates an increasing degree of self-organization going from monolayers to multilayers. Within the multilayer samples, the stacking sequence of the hexagonally packed layers is evaluated using a numerical model for fitting the X-ray scattering data containing the stacking parameter, a. Compared with an expected complete random stacking with a = 0.5, the fitted stacking parameter, a = 0.63 ± 0.01, averaged over a sample area of about 1 mm(2) indicates a preference for a cubic stacking sequence. This value is smaller than reported by various local probe techniques.