The effect of In surface segregation on the microstructure of short period superlattices (SPSs) in two different material systems with nominally equivalent lattice misfit, AlAs/InAs and GaAs/InAs, has been investigated and compared. It was found that the quality of the SPSs and the appearance of lateral composition modulation are remarkably different in these two systems. For AlAs/InAs SPSs grown at temperatures of T=500 °C,T=500 °C, uniform structures devoid of lateral composition modulation were obtained. Samples grown at T>500 °CT>500 °C exhibit lateral composition modulation. Uniform and homogeneous SPS structures were not obtained in the GaAs/InAs structures over the entire temperature range examined in this study (475 °C⩽T⩽510 °C).(475 °C⩽T⩽510 °C). Instead, lateral composition modulation with varying degrees of regularity was always observed. It was found that In segregation and roughening determine the microstructure. A kinetic exchange model predicts that at an optimum temperature the SPS layers are more intermixed for the AlAs/InAs SPSs. Thus, the lattice mismatch is lower and the driving force for roughening is reduced, resulting in uniform SPS structures. Growing the structure away from the optimum temperature for smooth growth may induce roughening-driven composition modulation. The GaAs/InAs structures are less intermixed over the temperatures studied, which results in higher mismatch between the individual layers and a higher driving force for roughening and lateral composition modulation. © 2002 American Institute of Physics.