A new low profile waveguide band-rejection filter (BRF) is proposed. In the waveguide BRF, substrate integrated waveguide (SIW) cavities are employed as resonators, and they are simply inserted in a hollow waveguide. For this simple configuration, this waveguide BRF is low-profile and easy to fabricate compared with a conventional waveguide BRF, which employs resonant waveguide cavities outside the waveguide and needs costly machining processes to fabricate. A Q-band prototype waveguide BRF is fabricated using alumina substrates and the measured results showed high attenuation more than 50 dB at 47 GHz in 2% fractional bandwidth.