Atomic force microscopy was used to study the morphology of GaAs buffer layers and the density and height distributions of self-assembled InGaAs quantum dots (QDs) grown on these buffers by molecular-beam epitaxy. The surface roughness and terrace size of 500 nm thick buffers were found to be independent of substrate preparation technique, but did vary depending on whether the buffers were grown either continuously, with a pulsed start, or with a final anneal. A short anneal at the QD growth temperature increased both the size of the surface features and the height of mounds on the buffer grown with a pulsed start. The variations in dot distributions on these three buffer types were similar, indicating that the length of step edges does not determine the density of QDs. The standard deviation in dot density was found to vary from 16 to 28% of the average dot density across the central 26 X 26 rum 2 region of the 5 cm wafers. The standard deviation in dot height was 10% or less of the average height. An inverse relationship was found between the dot height and density distributions, suggesting that a uniform amount of QD material was deposited on the wafers, but that the nucleation of the dots was nonuniform.