We report the most common single-nucleotide substitution/deletion mutations in favorable histology Wilms tumors (FHWTs) to occur within SIX1/2 (7% of 534 tumors) and microRNA processing genes (miRNAPGs) DGCR8 and DROSHA (15% of 534 tumors). Comprehensive analysis of 77 FHWTs indicates that tumors with SIX1/2 and/or miRNAPG mutations show a pre-induction metanephric mesenchyme gene expression pattern and are significantly associated with both perilobar nephrogenic rests and 11p15 imprinting aberrations. Significantly decreased expression of mature Let-7a and the miR-200 family (responsible for mesenchymal-to-epithelial transition) in miRNAPG mutant tumors is associated with an undifferentiated blastemal histology. The combination of SIX and miRNAPG mutations in the same tumor is associated with evidence of RAS activation and a higher rate of relapse and death. •FHWTs show recurrent mutations of both members of the miRNA microprocessor complex•DROSHA/DGCR8 mutant FHWTs show decreased expression of mir-200 family and Let7-a•SIX1/2 homeodomain mutations result in increased expression of CCND2•Undifferentiated histology predominates in SIX1/2, DROSHA, and DGCR8 mutant tumors Walz et al. identify recurrent SIX1, SIX2, DROSHA, and DGCR8 mutations in pre-therapy favorable histology Wilms tumors and find that mutant tumors more often have blastemal histology. Importantly, patients whose tumors have SIX1 or SIX2 mutations together with DROSHA or DGCR8 mutations have poorer survival.