We consider the process of Faraday rotation in femtosecond laser direct-write waveguides. The birefringence commonly associated with such waveguides may be expected to impact the observable Faraday rotation. Here, we theoretically calculate and experimentally verify the competition between Faraday rotation and birefringence in two waveguides created by laser writing in a commercial magneto-optic glass. The magnetic field applied to induce Faraday rotation is nonuniform, and as a result, we find that the two effects can be clearly separated and used to accurately determine even weak birefringence. The birefringence in the waveguides was determined to be on the scale of Δn = 10-6 to 10-5. The reduction in Faraday rotation caused by birefringence of order Δn = 10-6 was moderate and we obtained approximately 9° rotation in an 11 mm waveguide. In contrast, for birefringence of order 10-5, a significant reduction in the polarization azimuth change was found and only 6° rotation was observed.