HgCdTe is the most widely used material for high performance infrared detection applications. Growth of HgCdTe epitaxial layers by molecular beam epitaxy (MBE) has ushered in advanced devices that take advantage of the unique properties of the material. Formation of defects during the growth process is one of the largest drawbacks to this technology, and must be minimized to increase device operability. In this paper, the defects encountered in HgCdTe are categorized, along with formation mechanisms and possible means of reduction. A new method of defect identification is proposed, which takes advantage of full wafer defect mapping capabilities. A correlation between the thickness of the grown film and the size of defects initiated at the substrate surface is found. This allows further defect information to be extracted from the size and density of the defects.