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Abstract Background There is lack of evidence regarding safety, effectiveness and applicability of prehabilitation on cardiac surgery population, particularly in patients candidates to cardiac valve replacement. The aim of the study is to assess and compare the effect of a multimodal prehabilitation program on functional capacity in patients with severe aortic stenosis (AoS) and severe mitral regurgitation (MR) proposed for valve replacement surgery. Methods Secondary analysis from a randomised controlled trial whose main objective was to analyze the efficacy of a 4–6 weeks multimodal prehabilitation program in cardiac surgery on reducing postoperative complications. For this secondary analysis, only candidates for valve replacement surgery were selected. The primary outcome was the change in endurance time (ET) from baseline to preoperative assessment measured by a cycling constant work-rate cardiopulmonary exercise test. Results 68 patients were included in this secondary analysis, 34 (20 AoS and 14 MR) were allocated to the prehabilitation group and 34 (20 AoS and 14 MR) to control group. At baseline, patients with AoS had better left systolic ventricular function and lower prevalence of atrial fibrillation compared to MR (p = 0.022 and p = 0.035 respectively). After prehabilitation program, patients with MR showed greater improvement in ET than AoS patients (101% vs. 66% increase from baseline). No adverse events related to the prehabilitation program were observed. Conclusions A 4–6 week exercise training program is safe and overall improves functional capacity in patients with severe AoS and MR. However, exercise response is different according to the cardiac valve type disfunction, and further studies are needed to know the factors that predispose some patients to have better training response. Trial registration The study has been registered on the Registry of National Institutes of Health ClinicalTrials.gov (NCT03466606) (05/03/2018).