The rapid accumulation of new knowledge on the genes, gene variations and genetic loci associated with both forms of inflammatory bowel disease (IBD), e.g. Crohn’s disease (CD) and ulcerative colitis (UC), is shedding new light on the immunopathogenic mechanisms underlying these conditions. After the initial report of the association of NOD2 mutations with ileal CD, a large number of additional genetic variants and loci has been found to be associated with both CD and UC, CD alone and, quite recently, UC-associated variants have also emerged. Much of this progress is due to the use of methods such as genome-wide associations (GWA) based on large numbers of reasonably well-characterized patient groups. Among several others, some of the most pathophysiologically relevant associations reported so far are with gene variants related to innate immunity, autophagy, apoptosis, Th1 and Th17 responses, T cell activation, and immunosuppression. Some of these associations have lent further support to previously construed disease mechanisms or disclosed brand new mechanisms, like in the case of the autophagy pathway. While this much progress is obviously welcome, it also brings new challenges. These include the fact that all the gene mutations uncovered so far only account for a minority of all IBD cases, the variable distribution of gene mutations among worldwide IBD populations, and the still unknown effects of gene-gene and gene-environment interactions. Nevertheless, there is no question that genetic information will be quickly utilized not only for a better understanding of IBD pathogenesis, but it will also soon be incorporated into the armamentarium of better diagnostic and therapeutic tools.