Proportion of carriers of at least one polymorphic PTPN22 rs2476601 allele in subjects with coexisting T1D and CD was significantly higher compared to CD (OR = 2.97, 95% CI = 1.14–7.75, P = 0.026), however the difference was no longer significant after adjustment for age at diagnosis, gender and HLA genotype (OR = 2.42, 95% CI = 0.82–7.12, P = 0.109). Here, PTPN22 is linked to type 1 diabetes mellitus.