Vitamin D status may influence the risk of developing metabolic diseases such as Type 2 diabetes (T2D), metabolic syndrome (MetS) and insulin resistance (IR). Several studies have assessed vitamin D in relationship with metabolic outcomes; however, results remain inconsistent. A systematic review and meta-analysis using multiple databases (MEDLINE, Web of Science and EMBASE), was performed up to 10 August 2012. Prospective studies reporting association of circulating or dietary vitamin D with incident T2D, MetS and IR outcomes were included. Relative risks (RR) were pooled using random effects and subgroup analysis by pertinent study-level characteristics was performed. A total of seventeen articles based on eighteen unique prospective studies, and comprising 210 107 participants with 15 899 metabolic events, collected during a median follow up of 10 years (range 3–22 years), were included. RR for individuals in top v. bottom thirds of baseline vitamin D were 0·81 (95% CI 0·71, 0·92); 0·86 (95% CI 0·80, 0·92); and 0·84 (95% CI 0·64, 1·12) for T2D, MetS and IR outcomes, respectively. Moderate heterogeneity was found between fourteen studies (I2 = 67%, P < 0·001) reporting on T2D. Findings were generally consistent across various study-level characteristics. In conclusion, vitamin D status at baseline in apparently healthy adults is inversely associated with future risks of T2D and MetS. Interventions aimed at maintaining adequate levels of vitamin D in addition to preventing deficiency may be a useful preventive measure for metabolic diseases. However, reliable evidence from carefully designed intervention studies, particularly those based on healthy populations, is needed to confirm observational findings.