To identify susceptible regions of the genome(quantitative trait loci; QTLs)controlling Autoimmune pancreatitis in a mouse model of the disease, we established an advanced intercross line originating from three inbred mouse strains: MRL/MpJ,BXD2,NZM and wild derived strain Cast. The fourth generation of outbred intercross mice was characterized phenotypically by scoring histopathological changes of the pancreas and genotyped (Illumina, USA).Five QTLs, regulating the severity of AIP, were identified, which mapped to chromosomes 2,4,5 and 6(with Logarithmic P values varied from 3.2 to 5.4).