Inflammatory bowel disease (IBD) is considered as genetic disease due to observation of familial clustering of cases, genetic anticipation between generations and phenotypic concordance of some clinical features within families. Current knowledge of genes/loci associated IBD was largely developed by genome wide association studies which is common disease-common variant analysis strategy. With heterogeneity character and disease incidence of 4.75/100,000/year for Crohn’s disease and 2.06/100,000/year for ulcerative colitis in pediatric population, targeted resequencing and whole exome sequencing for the identification of rare pathogenic variants in known or novel genes are becoming more applicable for IBD genetic studies. According to chromosomal locus of genetic susceptibility, IBD was classified into 28 subtypes. According to functions and pathogenesis, genes involved in IBD can be classified into three groups including inflammation, immune regulation, and cellular adhesion/epithelial barrier integration. Genes regulate cell cycle, dysplasia or adhesion may be associated with cancer development in patients with long-standing IBD. Identification of casual genes/variants will be significant for diagnosis, treatment, prevention, cancer surveillance and improved health care for IBD patients.