Current screening methods have poor specificity and sensitivity for detecting cardiac abnormalities that predispose young athletes to sudden death. Natriuretic peptides (NPs) show promise in screening asymptomatic populations for structural heart disease, but little is known about their use in student athletes. This study sought to describe the distribution and characteristics of NP levels in a population of college athletes and determine the relationship between NPs and the pre-participation exam (PPE) and hand-held echocardiography (HHE). We evaluated 457 college varsity athletes with B-type NP (BNP) and N-terminal proBNP (NT-proBNP) levels and a standard PPE; 200 also underwent HHE. NT-proBNP and BNP levels were highly correlated (r=0.87, p<0.001), with a median of 21 pg/ml and 8 pg/ml respectively. 95% of athletes had NT-proBNP<84 pg/ml and 95% had BNP<33 pg/ml. Levels were higher in athletes with a history of exertional dizziness/syncope but did not correlate with other elements of the PPE or with HHE, although no major cardiac structural abnormalities were identified in this population. In men, there were weak correlations between NP levels and number of days per week performing distance running, strenuous exercise, or sprinting. In conclusion, NPs are only weakly correlated with intensity of physical training, and most college athletes have low NP levels; further studies are needed to elucidate the significance of elevated NP levels in this population, as they may provide incremental information beyond that provided by the PPE and echocardiography.