Abstract In this paper, we investigate the effective condition numbers for the generalized Sylvester equation (AX - YB, DX - YE) = (C,F), where A,D ∈ Rm×m B,E ∈ Rn×n and C,F ∈ Rm×n. We apply the small sample statistical method for the fast condition estimation of the generalized Sylvester equation, which requires (9(m2n + mn2) flops, comparing with (-O(m3 + n3) flops for the generalized Schur and generalized Hessenberg- Schur methods for solving the generalized Sylvester equation. Numerical examples illustrate the sharpness of our perturbation bounds.