Glomerulonephritis (GN) has been associated with many solid and hematologic malignancies. However, cancer prevalence at the time of GN diagnosis has been rarely examined. We aimed to evaluate the cancer prevalence in patients with GN at the time of kidney biopsy and to compare the results to those of the general population. A total of 1,155 patients who underwent kidney biopsy between 2003 and 2017 were included. We investigated patients diagnosed with cancer within one month of kidney biopsy. The occurrence of cancer was compared with that of the Korean general population using the observed-to-expected rates (O/E ratio). Twenty-nine patients with GN had cancer. The mean age of patients with and without cancer was 49 and 66 years old, respectively. The proportion of male patients with and without cancer was 49.4% and 58.6%, respectively. The glomerular filtration rate was different between the groups (78.1 ± 37.0, 58.0 ± 43.6 ml/min/1.73 m2, p = 0.006), but the urine protein/creatinine ratio was not (3.21 ± 4.01, 5.38 ± 7.47 g/gCr, p = 0.172). Immuno-globulin A nephropathy (IgAN) was the most common GN (37.9%), followed by membranous GN (13.5%), focal segmental glomerulosclerosis (9.7%), minimal change disease (9.2%), amyloidosis (1.2%). Amyloidosis was the most common GN associated with malignancy (20.7%). In patients with amyloidosis, cancer was observed almost 28 times more than expected and these patients showed higher cancer occurrence than patients with other GN (Relative Risk [RR]: 15.73; 95% confidence interval [CI]: 4.82–51.30; p < 0.01). Cancer occurrence was three times greater in GN patients aged > 50 years compared to the general population (O/E ratio: 3.42; 95% CI: 1.37–5.46; p = 0.027). Patients with GN, especially amyloidosis, have higher risk of cancer than the general population at the time of GN diagnosis. Older age (> 50 years) was one of the major determinants of the presence of cancer in GN patients.