The aim of the present study was to examine the effects of epithelial-mesenchymal transition (EMT) and apoptosis of renal tubular epithelial cells on the prognosis of immunoglobulin A (IgA) nephropathy. Renal biopsy tissues from 74 cases of IgA nephropathy were divided into a mild mesangial proliferation group (27 cases), a focal hyperplasia group (28 cases) and a proliferative sclerosis group (19 cases). The blood pressure, serum creatinine and 24 h urinary protein excretion of all patients were detected. To define EMT, α-smooth muscle actin (α-SMA), vimentin and collagen fibers were assessed. Apoptosis was determined by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL). The blood pressure, serum creatinine and 24 h urinary protein excretion of patients with IgA nephropathy altered with increasing pathological grade. All clinical indices of patients in the proliferative sclerosis group were higher than those of the other two groups, and the 24 h urinary protein excretion of the focal hyperplasia group was statistically higher than that of the mild mesangial proliferation group. The expression of tubular interstitial α-SMA, vimentin and collagen fibers increased with the pathological grade and was closely correlated with clinical indices, including collagen fibers and 24 h urinary protein excretion. TUNEL-positive cells increased with the exacerbation of pathological changes. The EMT and apoptosis of renal tubular epithelial cells reflected the clinical severity of IgA nephropathy. α-SMA, vimentin and the apoptotic index may be used as important markers for evaluating the prognosis of IgA nephropathy.