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This study investigated the association between habitual consumption of allium vegetables (garlic and onion) and the incidence of cardiovascular disease (CVD) outcomes, hypertension (HTN), chronic kidney disease (CKD), and type 2 diabetes (T2D).Adult men and women, participated in the Tehran Lipid and Glucose Study (2006–2008 to 2012–2014), were recruited. Habitual dietary intakes were assessed using a validated semiquantitative food frequency questionnaire. Demographics, anthropometrics, blood pressure, and biochemical variables were evaluated at baseline and during follow-up examinations. Multivariate Cox proportional hazard regression models adjusted for potential confounders were used to estimate the development of CVD outcomes, HTN, CKD, and T2D in relation to allium vegetable intakes.Mean age of participants (44.2% men) was 40.3 ± 14.3 years, at baseline. During an average of 6 years of follow-up, the incidence rate of CVD outcomes, HTN, CKD, and T2D were 3.3, 15.5, 17.9, and 6.7%, respectively. A higher habitual intake of allium vegetables was associated with a 64% reduced risk of CVD outcomes (hazard ratio = 0.36, 95% confidence interval, CI = 0.18–0.71; P for trend = 0.011), 32% lower incidence of CKD (hazard ratio = 0.69, 95% CI = 0.46–0.98; P for trend = 0.11), and 26% decreased HTN development (hazard ratio = 0.74, 95% CI = 0.54–1.00; P for trend = 0.06). No significant association was observed between allium vegetable intakes and the risk of T2D. Allium vegetable intake was related to 6 years’ changes of triglyceride levels (β = −0.81, P = 0.01) and creatinine clearance (β = 0.56, P = 0.01).Data of the current study support the available mechanistic findings regarding cardiorenal protective properties of allium vegetables.