IgG4-related disease (IgG4-RD) has been proved to be associated with malignancy.The incidence and risk factors of malignancy development in IgG4-RD were not clear. Nine IgG4-RD patients with malignancies and 27 IgG4-RD control cases were analyzed for risk factors and clinical features. The incidence of malignancy in IgG4-RD was 3.3%, higher than age-controlled general population. Smoking history was significantly more common in patients with malignancies than in the control group (9/9 vs 16/27, P<0.05). A total of 6/9 malignancies occurred within the first year after the diagnosis of IgG4-RD. Colorectal, biliary and thyroid cancers were the leading types. Smoking history is a risk factor for IgG4-RD associated malignancy. Careful vigilance to monitor malignancy needs to be paid during follow-up.