In this paper we describe a system that measures the attenuation and isolation of optical waveguides and has the capability to fully explore these properties over a range of reproducible launch conditions. The system allows both the launch signal spot size and numerical aperture to be varied and can be correlated to the actual operating conditions of the board. Characterization of the optical system, including the magnification factor as well as the linearity, sensitivity, spatial uniformity of the charge-coupled device cameras, is shown. Initial results from a variety of waveguides, including planar, radii, and crossover designs, are discussed and an assessment of the key uncertainty contributions of the system is presented.