The optical waveguides in Bi(4)Ge(3)O(12) (BGO) crystals in both depressed-cladding and dual-line configurations have been produced using femtosecond-laser micromachining. The guiding properties and thermal stabilities of the BGO waveguides have been investigated for both geometries, showing different performance of the fabricated structures. Both depressed-cladding and dual-line waveguides support guidance along both TE and TM polarizations. Thermal annealing treatments up to 600°C reduce the propagation loss of dual-line waveguides to as low as 0.5 dB/cm, while the cladding waveguide is only stable under thermal treatment not higher than 260°C, reaching a propagation loss of 2.1 dB/cm.