Disclosed is a system and methodologies for providing self-calibration in an optical analysis system. Illumination light is directed toward a material to be sampled while provisions are made to modify the characteristics of at least a portion of the illumination light falling on a reference detector. The modified characteristics may include light presence and/or spectral characteristics. Light presence may be modified by rotating or moving mirror assemblies to cause light to fall on either a sample detector or a reference detector while spectral characteristics may be modified by placing materials having known spectral characteristics in the path of the illumination light.