<b><i>Background:</i></b> MicroRNAs (miRNAs) play important roles in the progression of renal fibrosis. We studied the urinary levels of miR-21, miR-29 family and miR-93, which are downstream mediators of the transforming growth factor-β₁ (TGF-β₁), in patients with immunoglobulin A (IgA) nephropathy. <b><i>Methods:</i></b> We studied the urinary miRNA levels of 43 IgA nephropathy patients and 13 healthy controls. <b><i>Results: </i></b>The IgA nephropathy group had significantly lower urinary miR-29b and miR-29c, but higher miR-93 levels than controls. Proteinuria significantly correlated with urinary levels of miR-29b (r = –0.388, p = 0.003) and miR-29c (r = –0.409, p = 0.002). Glomerular filtration rate significantly correlated with urinary levels of miR-21 (r = 0.338, p = 0.028), miR-29b (r = 0.333, p = 0.031) and miR-29c (r = 0.304, p = 0.050). Urinary miR-93 level significantly correlated with glomerular scarring (r = –0.392, p = 0.010). Urinary miRNA level of SMAD3, but not TGF-β₁, correlated with urinary miR-21 (r = 0.624, p < 0.001), miR-29b (r = 0.566, p < 0.001), miR-29c (r = 0.619, p < 0.001) and miR-93 (r = 0.332, p = 0.032). <b><i>Conclusions:</i></b> Urinary miR-29b and miR-29c levels correlated with proteinuria and renal function, while urinary miR-93 level correlated with glomerular scarring. More importantly, urinary levels of these miRNA targets significantly correlated with urinary SMAD3 level. Our results suggest that these miRNA targets are regulated by the TGF-β₁/SMAD3 pathway and they may play important roles in the development of progressive renal fibrosis in IgA nephropathy.