Strenuous exercise results in transient but minor alterations in left ventricular diastolic function (LVDF). The aim of this study is to describe and interpret the kinetics of the well-established 2D parameters of diastolic function and the novel and very sensitive 3D parameters before/after a marathon race. LVDF was evaluated by transthoracic echocardiography (TEE) in 212 healthy male [aged 42 (36–49) years)] marathon runners (all Be-MaGIC-study) in the week prior to (V1), immediately after (V2), 24 h after (V3) and 72 h after (V4) a marathon race. Real time three-dimensional echocardiography (RT3DE) included maximal and minimal left atrium (LA) volume, total LA ejection fraction (Total-EF), total LA stroke volume (Total-SV), true ejection fraction (True-EF) and atrial stroke volume (ASV). After adjustment for possible confounders (heart rate and systolic blood pressure), 2D Parameters of left ventricular inflow (E/A-ratio) decreased from pre- to immediately post-race (− 0.3 ± 0.06, p < 0.001) and returned to baseline within 24 h. \({\text{E}}/{{\text{e}^{\prime}}}_{{{\text{mean}}}}\)-ratio remained unchanged directly post-race, but was significantly increased during follow-up of 24 and 72 h. 3D LA V_min was increased immediately postrace and in the 24 h follow-up, LA V_max was increased immediately post-race and in the follow-up of 24 and 72 h. During follow-up of 72 h, but not immediately postrace, TrueEF and ASV were significantly increased. Both techniques revealed acute and prolonged alterations of diastolic LV function. Considering all parameters, the recovery of diastolic LV after a marathon seems to take longer than previously assumed.