If one or more types of a person's colour-sensing cones are missing or less responsive than normal to incoming light, that person has a smaller or skewed colour space and is said to be colour deficient. Another term frequently used is "colour blind", although this can be misleading; only a small fraction of colour deficient individuals actually see completely in black and white, and most simply have anomalous colour perception.

Some kinds of colour deficiency are caused by anomalies in the number or nature of cones of the various types, as just described. Others are caused by neural anomalies in those parts of the brain where visual processing takes place.

Some animals may have more than three different types of colour receptors (most marsupials, birds, reptiles and fish) or fewer (most mammals; these are called dichromats and monochromats). Humans and other 'old-world' primates are actually rather unusual in possessing three kinds of receptors.

An unusual and elusive neurological condition sometimes affecting colour perception is synaesthesia - stimulation of one sensory modality gives rise to an experience in another modality. In an auditory synaesthete, for example, an auditory experience may give rise to an experience in the visual modality