The propagation losses of the straight waveguide in three-dimensional photonic crystals with finite thickness have been estimated by using the finite-difference time-domain method. It was confirmed that the propagation loss decreases almost exponentially as the thickness of the photonic crystal increases. The waveguide for the photonic crystal suspended in air has complicated transmission properties, although it achieves the efficient guiding of light. For the six-stacking-period- or 24-layer-thick photonic crystal suspended in air, the propagation loss of less than 1 dB/mm was evaluated in a wide wavelength range around 1.55 µm. Our results indicate that to obtain the loss of the same order, we can use photonic crystals surrounded on both sides by GaAs, which have an advantage in terms of stability for the construction of large-scale crystals, by increasing the thickness by one extra period.