The A allele of rs12803915 in premature mir-612 was found to be protective (GG vs. GA vs. AA; OR, 0.61; 95% CI: 0.42 to 0.88; p = 0.007) against ALL risk. The G allele of rs3746444 in the seed region of mature miR-499-3p was also found to be protective (AA vs. AG vs. GG; OR, 0.67; 95% CI: 0.49 to 0.91; p = 0.009). An association with rs10061133 in mir-449b was also identified (AA vs. GA+GG; OR, 0.52; 95% CI: 0.31 to 0.89; p = 0.012). Eight SNPs present in the six miRNA biogenesis pathway genes (TNRC6B, DROSHA, DGCR8, EIF2C1 or AGO1, CNOT1 and CNOT6) were also identified. The gene discussed is CNOT1; the disease is acute lymphoblastic leukemia.