Background: Although great efforts have been paid on identification of genetic predisposition in the inherited retinal disease (IRD), genetic causes of a large proportion of patients remain a mystery. This dilemma makes us attempt to speculate that genetic components other than coding genes might be an additional pool predisposing IRD. In this study, we aim to perform a mutational screening in a large cohort of IRD patients with a particular focus on retina-specific or abundant microRNAs (miRs). Material and methods: A total of 324 unrelated patients with IRD were recruited. Targeted next-generation sequencing (tNGS) was performed to survey genetic mutations in 32 known miRs highly expressed in the retina, followed by validation with Sanger sequencing, co-segregation analysis in each family, and computational assessments. Results: Novel genotype-phenotype associations have been uncovered. In total, six different variants in the miRs were identified, including four rare ones, miR-216a (n.56C>A), miR-216b (n.43_44insG), miR-7-2 (n.107C>T), and miR-7-3 (n.95G>A). The other two variants, miR-182 (n.106G>A) and miR-216a (n.105T>A), were considered as polymorphic. Conclusions: We for the first time screened candidate retinal miRs in patients with IRD. Although there is no convincing evidence that these variants are responsible for the IRD, the results enhance the current knowledge of the associations between IRD and miRNAs variants.