The impact of positional and radial disorders on the transmission spectrum of photonic crystal waveguides with different shapes of air-holes, including circular, square and elliptic were numerically investigated. It was found that the disorder affects the anti-crossing point greatest. The flat transmission spectrum becomes narrower as disorder increasing. The transmission property performs more sensitive on the air-holes positions than radii. The square air-holes are more robust against the positional disorder. The circular air-holes are more robust alainst the radial disorder. These results provide important theoretical instructions on the imperfection during the manufacture possess in the PCWs experiment.