ABSTRACT. Spectral automorphisms have been introduced in [IVANOV, A.-CARAGHEORGHEOPOL, D.: Spectral automorphisms in quantum logics, Internat. J. Theoret. Phys. 49 (2010), 3146-3152] in an attempt to construct, in the abstract framework of orthomodular lattices, an analogue of the spectral theory in Hilbert spaces. We generalize spectral automorphisms to the framework of effect algebras with compression bases and study their properties. Characterizations of spectral automorphisms as well as necessary conditions for an automorphism to be spectral are given. An example of a spectral automorphism on the standard effect algebra of a finite-dimensional Hilbert space is discussed and the consequences of spectrality of an automorphism for the unitary Hilbert space operator that generates it are shown.The last section is devoted to spectral families of automorphisms and their properties, culminating with the formulation and proof of a Stone type theorem (in the sense of Stone's theorem on strongly continuous one-parameter unitary groups -see, e.g. Orthomodular lattices and orthomodular posets have been considered for a long time to be the appropriate mathematical structures for studying the logic of quantum mechanics [13,14]. To allow the study of unsharp measurements or observations, represented by quantum effects, the algebraic structure of effect algebra is currently used (see, e.g., [2,4]). The so-called compressions were introduced by Gudder [7] in the framework of effect algebras as an abstraction of 2010 M a t h e m a t i c s S u b j e c t C l a s s i f i c a t i o n: Primary 81P10; Secondary 81Q10. K e y w o r d s: spectral automorphism, effect algebra, compression base, CB-effect algebra, spectral theory, effect algebra automorphism. The author gratefully acknowledges the scholarship of the Czech Technical University in Prague.