The amphoteric native defect model of the Schottky barrier formation is used to analyze the Fermi level pinning at metal/semiconductor interfaces for submonolayer metal coverages. It is assumed that the energy required for defect generation is released in the process of surface back‐relaxation. Model calculations for metal/GaAs interfaces show a weak dependence of the Fermi level pinning on the thickness of metal deposited at room temperature. This weak dependence indicates a strong dependence of the defect formation energy on the Fermi level, a unique feature of amphoteric native defects. This result is in very good agreement with experimental data. It is shown that a very distinct asymmetry in the Fermi level pinning onp‐ andn‐type GaAs observed at liquid nitrogen temperatures can be understood in terms of much different recombination rates for amphoteric native defects in those two types of materials. Also, it is demonstrated that the Fermi level stabilization energy, a central concept of the amphoteric defect system, plays a fundamental role in other phenomena in semiconductors such as semiconductor/semiconductor heterointerface intermixing and saturation of free carrier concentration.