ABSTRACT Background With accruing case reports on de novo or relapsing glomerular diseases (GD) following different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, we evaluated the risk of GD following BNT162b2 and CoronaVac vaccines. Methods A modified self-controlled case series analysis was conducted using anonymized, territory-wide SARS-CoV-2 vaccination records in Hong Kong. All Hong Kong residents aged 18 years or above with outcomes of interest were included. Outcomes of interest were GD, proteinuria or hematuria within 42 days following each dose of SARS-CoV-2 vaccines. Incidence per 100 000 doses of SARS-CoV-2 vaccines administered was calculated, and incidence rate ratios (IRRs) were estimated using conditional Poisson regression with seasonality adjustment. Results Between 23 February 2021 and 31 March 2022, 4062 patients had an incident diagnosis of GD, proteinuria or hematuria, with 2873 of them being vaccinated during the observation period. The incidences of the composite events 1–41 days after vaccination were 3.7 (95% CI 3.1–4.4) per 100 000 doses of BNT162b2 administered, and 6.5 (95% CI 5.7–7.5) per 100 000 doses CoronaVac administered. There was no significant increase in the risks of composite events following the first (BNT162b2: IRR = 0.76, 95% CI 0.56–1.03; CoronaVac: IRR = 0.92, 95% CI 0.72–1.19), second (BNT162b2: IRR = 0.92, 95% CI 0.72–1.17; CoronaVac: IRR = 0.88. 95% CI 0.68–1.14) or third (BNT162b2: IRR = 0.39. 95% CI 0.15–1.03; CoronaVac: IRR = 1.18. 95% CI 0.53–2.63) dose of SARS-CoV-2 vaccines. Conclusions There was no evidence of increased risks of de novo or relapsing GD with either BNT162b2 or CoronaVac vaccines.