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Physical activity (PA) in the daily life is strongly related to prognosis in patients with or at high risk of heart failure (HF). However, factors limiting habitual exercise and their prognostic impacts remain unknown in HF patients. We sent questionnaires asking factors limiting habitual exercise in the daily life to 8370 patients with Stage A/B/C/D HF in our nationwide registry and received valid responses from 4935 patients (mean age 71.8 years, 71.0% male). Among the 5 components consisting of “busyness”, “weak will”, “dislike, “socioeconomic reasons” and “diseases” in the questionnaires, “busyness” (34.5%) and “diseases” (34.7%) were the most frequently reported factors limiting habitual exercise, while “socioeconomic reasons” were the least (15.3%). Multiple Cox proportional hazard models indicated that “busyness”and “diseases” were associated with better (hazard ratio (HR) 0.53, 95% confidence interval (CI) 0.39–0.72, P  < 0.001) and worse prognosis (HR 1.57, 95% CI 1.21–1.98, P  < 0.001), respectively, while other components were not. Furthermore, it was noted that, while prognostic relevance of “busyness” limiting exercise did not differ by age or sex, negative impact of “diseases” was particularly evident in patients with age < 75 years ( P for interaction < 0.01). Factors limiting habitual exercise were associated with “busyness” and “diseases”, but not with “weak will”, “dislike, or “socioeconomic reasons”. While “busyness” was associated with better prognosis regardless of age and sex, “diseases” was associated with worse prognosis in younger populations. Thus, physicians may pay more attentions to the reasons that limit exercise in the daily lives of HF patients rather than the low amount of exercise itself.