In the present study, we investigated whether potential loci reported in the meta-analysis and GWA studies on chromosomes 5p13 (PTGER4), 12q15 (IFNG, IL22, IL26), 6p21 (HLA), 21q22 (PSMG1), and PTPN2, NKX2-3, TNFSF15, were associated in a large and phenotypically well-characterized Italian cohort of IBD patients, and we also attempted to elucidate their involvement in early onset disease. Here, PTPN2 is linked to inflammatory bowel disease.