The effects of the thickness of GaAs spacer layers on the structure of multilayer stacked InAs quantum dots (QDs) grown by molecular-beam epitaxy were studied using transmission electron microscopy. To investigate QD structure depending on spacer layer growth, first uncapped free-standing QDs were grown and their structure compared with that of multilayer stacked QDs. In addition, vertically nonaligned and aligned stacked QDs were grown by adjusting the thickness of GaAs spacer layers. The uncapped QDs were found to form a lens-shaped structure with side facets. Upon capping with a GaAs spacer, the apex of nonaligned QDs flattened by In diffusion. However, the aligned QDs maintained their lens-shaped structure with round apex after capping. it is believed that their apex did not flatten because the chemical potential gradient of In was relatively low due to the adjacent InAs QD layers. The results demonstrate the possibility of controlling QD structure by adjusting the thickness of spacer layers. (C) 2008 Published by Elsevier B.V.