Purpose. Various studies have shown an association between miRNA polymorphisms and susceptibility to autoimmune disease (AD); however, the results are inconclusive. To evaluate whether miRNA polymorphisms account for a significant risk of AD, a total of 87 articles, including 39431 patients and 56708 controls, were identified to estimate their association with 12 AD subtypes. Methods. Several electronic databases were searched to analyze population-based studies on the relationship between miRNA variants and AD risk. Fixed effects or random effect models were used in the meta-analysis for the risk assessment. Results. In our meta-analysis, miR-146a rs2910164/rs57095329 conferred a marginally elevated risk for AD (allele model,
OR
=
1.08
, 95% CI: 1.01-1.15,
P
=
0.019
; allele model,
OR
=
1.09
, 95 CI: 1.05-1.15,
P
<
0.001
, respectively). Furthermore, miR-196a2 rs11614913 was also associated with AD risk (allele model,
OR
=
0.92
, 95% CI: 0.88-0.97,
P
=
0.001
) as well as miR-499 rs3746444 (allele model,
OR
=
1.16
, 95% CI: 1.03-1.29,
P
=
0.011
). In addition, associations were observed between miR-149 rs2292832/miR-27a rs895819 and AD susceptibility in the overall population (allele model,
OR
=
1.15
, 95% CI: 1.06-1.24,
P
<
0.001
; allele model,
OR
=
1.11
, 95% CI:1.01-1.22,
P
=
0.043
, respectively). Conclusions. Evidence from our systematic review suggests that miR-146a, miR-196a2, miR-499, miR-149, and miR-27a polymorphisms are associated with susceptibility to AD.