Objective: To determine the correlation of IgM deposition with clinic-pathological features and outcomes of IgA nephropathy patients. Methods: A total of 1060 patients, who were diagnosed as IgA nephropathy by renal biopsies between 2001 and 2007 in Guangxing Hospital were enrolled. According to immunofluorescent test, patients were divided into patients with mesangial IgM deposition and patients without IgM deposition. Renal survival curves were assessed by Kaplan-Meier method. The effect of IgM deposition on outcomes of IgA nephropathy patients was examined by univariate and multivariable Cox proportional-hazards regression. Results: Among 1060 IgA nephropathy patients, there were 750 patients with IgM deposition and 310 patients without IgM deposition. (1) Urinary protein and uric acid in patients with IgM deposition were significantly higher than those in patients without IgM deposition (all P<0.05). Other clinical indicators shown no statistical difference (all P>0.05). Moreover, IgM deposition patients had higher serum IgA, serum IgG and serum IgM (all P<0.05). (2) In pathological indicators, IgM deposition patients had more segmented sclerosis or adhesions (S1 of Oxford classification), activity lesions as inflammatory cell infiltration and mesangial proliferation, and chronic pathological changes as tubular atrophy, segmented glomerular damage than patients without IgM deposition (all P<0.05). (3) All patients were followed-up for a median of 89.7(61.8, 113.4) months, Kaplan-Meier analysis revealed that kidney survival rate was significantly lower in IgM deposition patients compared with patients without IgM deposition (Log-rank χ²=4.95, P=0.026). In a univariate Cox hazards regression mode, IgM deposition was a risk factor for poor prognosis of IgA nephropathy patients (HR=1.597, 95% CI 1.053-2.422, P=0.027). However, in a multivariable Cox analysis, IgM deposition shown no influence on outcomes of IgA nephropathy patients (HR=1.409, 95% CI 0.921-2.156, P=0.114). Conclusions IgA nephropathy patients with IgM deposition have higher urinary protein, and more serious pathological damage and immune fluorescence deposition. IgM deposition affects renal survival of IgA nephropathy, while IgM deposition is not an independent risk factor for prognosis of IgA nephropathy.