Association of cardiovascular disease (CVD) with nontraditional risk factors such as vitamin D deficiency has been examined previously. An investigation of the association of vitamin D with subclinical myocardial injury (SC-MI) based on an electrocardiographic score is a simple, cost-effective and innovative way to explore this relationship. We hypothesize that low vitamin D levels will be associated with prevalent SC-MI independent of traditional CVD risk factors, lifestyle factors, and socioeconomic status. This analysis included 6079 participants (58.3 ± 13.1 years; 54.1% women) without CVD from the third National Health and Nutrition Examination Survey. A multivariable logistic regression model was used to examine the association between vitamin D categories (<20, 20-29, and >30 ng/mL (reference) and cardiac injury score. There was an incremental increase in the prevalence of SC-MI across vitamin D categories with the highest prevalence in <20 ng/mL, followed by 20 to 29 ng/mL and then >30 ng/mL (trend P-value <0.0001). There was a statistically significant association between vitamin D deficiency (<20 ng/mL) and SC-MI (odds ratio [OR] (95% confidence interval [CI]): 1.27 (1.04-1.55), P = 0.04). This association was stronger in men than women (OR (95% CI): 1.74 (1.32-2.30) vs 0.94 (0.70-1.25) respectively; interaction P-value 0.002). Vitamin D deficiency is associated with SC-MI, especially in men. These findings may further highlight the role of nontraditional risk factors in the development of CVD. The value of vitamin D supplementation in the prevention of myocardial ischemia and injury may warrant investigation.