The microstructures of annealed GaAs layers containing 0.1%, 0.5% and 2% Mn are studied using aberration-corrected transmission electron microscopy (TEM). The layers were grown by molecular beam epitaxy at 270 °C. After heat treatment at 400, 560 and 630 °C, they are found to contain precipitate complexes of cubic or hexagonal (Mn, Ga) As, orthorhombic or rhombohedral As and voids. Information about the crystallographic structures and compositions of the phases is obtained using high-resolution TEM, scanning TEM and energy-dispersive x-ray spectroscopy. A phase diagram for secondary phase formation in annealed GaMnAs layers doped with low Mn concentrations is proposed.