The nature and behavior of antiphase boundaries in GaAs/Si heterostructures using GaP, GaP/GaAsP, and GaAsP/GaAs strained‐layer superlattices as intermediate layers have been studied by transmission electron microscopy. The antiphase domains are found to be very complicated three‐dimensional polygons consisting of several subboundaries in different orientations. Self‐annihilation of antiphase domains during crystal growth of GaAs on (001) 0.4° off or (001) 2° off Si substrates is directly observed for the first time through plan‐view and cross‐sectional observations. Based on these findings, a mechanism of annihilation of these domains is presented.