Atherosclerosis is the main cause of death in the world through causing ischemic heart disease (IHD). Altered serum lipid level is the most important risk factor for coronary artery disease (CAD). Many studies reveal a strong inverse association between low levels of high density lipoprotein cholesterol (HDL-C) and increased risk of IHD. On the other hand, plasma levels of HDL-C has a strong hereditary basis. This review focuses on recent data about genetic defects that reduce the level of HDL-C. In order to investigate possible genes linked to low HDL-C disorder, we reviewed previous studies; we searched current medical literature from September 1990 through January 2013 for the genetics causes of low HDL-C levels. Genetic defects in ATP binding cassette protein (ABCA1), apolipoprotein (APO) A1, lecithin cholesteryl acyl transferase, Lipoprotein lipase (LPL), and angiopoietin-like 3 proteins (ANGPTL3) associated with low HDL-C. Other potentially important candidates involved in low HDL-C syndromes are metabolic disorders including sphingomyelin phosphodiesterase 1 and glucocerebrosidase. Also Molecular variations in many genes such as ABCAI and APOAI, TRIB1 and Apo E, lipoprotein lipase (LPL), WW domain-containing oxidoreductase (WWOX), Hepatic lipase (HL), lecithin cholesteryl acyl transferase and some linkage analysis have been associated with reduced HDL-Status. Low HDL-C syndrome has a strong genetic basis and is correlated with an increased risk of CAD.