Electron backscatter diffraction patterns obtained from low symmetry crystals can present difficulties for automated pattern recognition. For example, when only a single zone axis is observed in the diffraction pattern and the Kikuchi bands used for indexing all pass through the zone axis then only two-dimensional crystallographic information is obtained. This results in there being a 180 degree ambiguity in the measured orientation. Furthermore, it is often observed that in automated indexing of quartz, an additional ambiguity is introduced when the zone axis imaged is [0001]. In this case it is difficult to distinguish between the true orientation and it’s twin. This ambiguity is overcome only if Kikuchi bands from the upper Laue zones are used in the indexing. However, in automated indexing it is normal for the computer to select the strongest Kikuchi bands visible and these will not be those from the upper Laue zones when the [0001] zone axis is imaged. This and other pseudo symmetries have been observed and have been overcome by applying correction procedures during data collection and in post collection analysis.