Type 2 Diabetes is a major health care problem responsible for early morbidities and mortality. T2D prevalence inexorably increases due to dramatic changes in our way of life. T2D is preventable but no generally curable and present medications fail to prevent the worsening of glucose control and the development of complications. T2D is a systemic disease characterized by both insulin secretion defects and by insulin resistance at the levels of several tissues. Despite more than 40 years of research the aetiologies of T2D are still elusive. T2D is a multifactorial disease with a significant genetic component. However, T2D is a polygenic disorder with the effects of multiple DNA variants having a modest effect and a weak penetrance interaction with environmental factors. The identification of T2D susceptibility genes has been transformed by Genome Wide Association Studies (GWAS) which allow the analysis of hundred of thousands Single Nucleotide Polymorphisms (SNPs) in thousands of samples. Case/control GWAS have identified about 30 loci/genes, so far. However, these loci only explain a small part of T2D inheritance. T2D is defined by the measurement of the continuous trait “glycemia”. A fasting plasma glucose (FPG) higher than 7mM is considered to be abnormal. FPG is highly genetically determined and we have reanalyzed our GWAS data obtained in non diabetic general populations to identify genes that control (normal) glucose values. We first found that SNPs at MTNR1B (encoding the melatonin 2 receptor) locus regulate both FPG and insulin secretion. Melatonin is the hormone of darkness that plays a major role in circadian rhythms. The alteration of these physiological rhythms has been shown to impair glucose homeostasis. Subsequently we have screened and functionally analysed the coding part of MTNR1B in thousands of T2D cases and controls for rare lack of function mutations that strongly increase the risk for T2D. In addition via our contribution to the international consortium MAGIC we have identified 16 genetic markers modulating FPG, five controlling blood glucose after oral glucose load, and ten involved in the variance of glycated haemoglobin (HbA1c, a clinical marker of glucose control in treated diabetic patients). In this respect, we have demonstrated that if HK1 (encoding hexokinase 1) is the most potent gene controlling HbA1c, it was not at all involved in the physiology of glucose homeostasis. Instead, variant at HK1 locus act on red cell function, increase risk for anemia, and only indirectly perturb HbA1c measurement. This study shows that GWAS findings don’t mean causality and it is always mandatory to question the physiological validity of any association found through GWAS before implying a gene as causal. In this respect, the MAGIC consortium showed that among all the genes that regulate HbA1c, a large proportion is indeed directly related to red cell function. In conclusion, during my PhD, I have contributed to achieve a map of frequent SNPs regulating the major glucose control quantitative traits that define T2D. I also showed that rare DNA variants with a stronger biological impact also contribute to T2D risk. Although still of limited value for the prediction of T2D, GWAS have proven extremely useful to make progress in T2D physiology.