A generalization of down-up algebras was introduced by Cassidy and Shelton in [11], the so-called generalized down-up algebras. We describe the automorphism group of conformal Noetherian generalized down-up algebras L(f, r, s, γ) such that r is not a root of unity, listing explicitly the elements of the group. In the last section we apply these results to Noetherian down-up algebras, thus obtaining a characterization of the automorphism group of Noetherian down-up algebras A(α, β, γ) for which the roots of the polynomial X 2 − αX − β are not both roots of unity.