Vortex formation time (VFT) is a continuous measure of the left ventricular (LV) filling that integrates all phases of diastole. This has been previously studied in patients with heart failure. This study examined the differences in VFT between healthy controls and elite athletes. We compared echocardiographic indices between elite male athletes (n = 41) and age-, weight- and sex-matched sedentary volunteers (n = 22). VFT was obtained using the validated formula: 4 × (1 − β)/π × α³ × LVEF, where β is the fraction of total transmitral diastolic stroke volume contributed by atrial contraction (assessed by time velocity integral of the mitral E- and A-waves) and α is the biplane end-diastolic volume (EDV)^1/3 divided by mitral annular diameter during early diastole. Diastolic function was measured by the ratio of mitral peak velocity of early filling (E) to early diastolic mitral annular velocity (e′) (E/e′ ratio) and the ratio of E to mitral peak velocity of late filling (A) (E/A ratio). The heart rate was lower (63 ± 10 vs. 74 ± 6 beats per minute, p < 0.001) and the LV end diastolic diameter was larger in athletes as compared to controls (56 ± 3 vs. 50 ± 4 mm, p < 0.001). The VFT was lower in the sedentary group compared to athletes (3.1 ± 0.4 vs. 4.0 ± 0.8, p < 0.001). Similarly, E/e′ was higher in sedentary controls compared to athletes (7.5 ± 1.8 vs 4.2 ± 1.0, p < 0.001). Furthermore, there was a modest correlation between VFT and E/A (r = 0.47, p < 0.001) as well as E/e′ (r = − 0.33, p = 0.012). In conclusion, the VFT was elevated among elite athletes compared to healthy sedentary controls.