Instanton effects are considered for a sample of supersymmetric theories, namely, quantum mechanics, gluodynamics, Higgs model. The problem is how to reconcile the apparent lack of the boson-fermion symmetry in the effective instanton induced interactions with supersymmetry of the corresponding lagrangians. It is shown that in the case of quantum mechanics and the Higgs model there is actually no conflict between supersymmetry and the instanton calculus since the Ward identities, associated with the supersymmetry transformations, are satisfied. In quantum mechanics this is due to spontaneous symmetry breaking, or pole terms in matrix elements of supercharge, while in the case of the supersymmetric Higgs model the effective fermion interaction just reduces to a total derivative. In the case of supersymmetric gluodynamics, however, the standard instanton calculus explicitly violates naive Ward identities.