Germanium (Ge) nanocrystals embedded in silica matrix is an interesting material for new optoelectronic devices. In this paper, standard silica-on-silicon waveguides with a core doped by Ge nanocrystals were fabricated using plasma enhanced chemical vapour deposition and reactive ion etching. The cross-sectional waveguide structures were investigated by scanning electron microscopy. Transmission of the waveguide was measured using a broadband light source covering the wavelength range from 500 nm to 1700 nm, and the results were compared against transmission through a standard waveguide. Strong absorption peaks at 1056.8 nm, 1263.2 nm and 1406 nm were observed. These are assigned to the quantum confinement effect in Ge nanocrystals in the core. Putting Ge nanocrystals in a waveguide enables easy material characterisation and potential application in an integrated lightwave circuit device. PACS 42.82.-m · 42.50.-p · 1.07.Ta