It has been suggested that the rs2910164 and rs3746444 polymorphisms of pre-miRNA are significantly associated with the risk of autoimmune diseases (ADs), described as candidate susceptibility factors, whereas results have yield conflicting findings. We conducted this meta-analysis to investigate whether these two polymorphisms contribute to susceptibility to ADs by using allele comparison and different genetic models, and we also performed stratified analyses by ethnicity and disease phenotype. Our meta-analysis demonstrated that increased risk of ADs was significantly associated with GC genotype in Asians for SNP rs2910164 in the stratified analyses by ethnicity; there was increased OR for GC genotype compared with that for GG+CC genotype in other disease subgroup, respectively (OR=0.89, 95% CI=0.79-0.99; OR=0.84, 95% CI=0.75-0.95, respectively). Moreover, elevated AD risk was found to be associated with CC genotype of rs3746444 in contrast to TT and TT+TC carriers, respectively (OR=0.55, 95% CI=0.34-0.90; OR=0.59, 95% CI=0.36-0.97, respectively). Taken together, these findings indicated that the rs2910164 and rs3746444 polymorphisms may play potential roles in the pathogenesis of ADs.