Abstract. We study time-harmonic electromagnetic and acoustic waveguides, modeled by an infinite cylinder with a non-smooth cross section. We introduce an infinitesimal generator for the wave evolution along the cylinder and prove estimates of the functional calculi of these first order non-self adjoint differential operators with non-smooth coefficients. Applying our new functional calculus, we obtain a one-to-one correspondence between polynomially bounded time-harmonic waves and functions in appropriate spectral subspaces.Mathematics Subject Classification. Primary 47A10, 47A60, Secondary 35Q61, 35J05.