Quantum dot structures containing 2 and 7 layers of small coherent InAs clusters embedded into a Si single crystal matrix were grown by MBE. The structure of these clusters was investigated by high resolution transmission electron microscopy. The crystallographic quality of the structure severely depends on the substrate temperature, growth sequence, and the geometrical parameters of the sample. The investigation demonstrates that Si can incorporate a limited volume of InAs in a form of small coherent clusters about 3 nm in diameter. If the deposited InAs layer exceeds a critical thickness, large dislocated InAs precipitates are formed during Si overgrowth accumulating the excess of InAs.