Waveguide apparatus for use in substance analysis has a waveguide, with a surface area in contact with the substance, for transmitting electromagnetic radiation along the axis of the waveguide whereby propagation characteristics of the radiation are altered in accordance with properties of the substance adjacent the waveguide. A waveguide entrance prism is positioned at the radiation entrance end of the waveguide, for guiding radiation into the waveguide. The prism has a first face arranged at an angle with the waveguide axis to cause radiation entering the prism to propagate along the waveguide. In one embodiment, a longitudinal partition is arranged adjacent the waveguide substantially parallel to the waveguide axis, for partitioning the waveguide surface area into at least two parts so that multi-substance analysis can be carried out. In another embodiment, the waveguide entrance prism includes a first face perpendicular to the waveguide axis, and second and third faces at an angle to both the waveguide axis and the first face. In effect, two entrance prisms are provided in the second embodiment. The second embodiment also includes a reflector and filter at the distal end of the waveguide to filter and reflect radiation back to the entrance prism.