BACKGROUND: The aims of this study were to analyze the effects of the COVID-19 pandemic and its subsequent confinement on behaviors, perception of threat, stress, state of mind and training patterns among Olympic and Paralympic level athletes. METHODS: Data gathering was performed utilizing an online questionnaire during imposed confinement. A correlational design with incidental sampling for convenience was used. All the variables were analyzed by age, gender, academic training, type of participation and sport specialty on a population composed of 447 Olympic (age: 26.0 ± 7.5 years) and 64 Paralympic (age: 28.4 ± 10.5 years) athletes. RESULTS: The athletes trained more than twice as many hours before than during confinement. Most of the athletes recognized that their best athletic performance diminished due to the COVID-19 confinement but that will recover after the pandemic and its confinements. Almost half of the athletes declared they were more tired than normal and had difficulty sleeping, while more than half ate more or less as usual. Paralympic athletes reported they felt more capable to cope with personal problems and life events and felt less lonely during the confinement than the Olympians. The athletes from team sports reported to be more affected in their training routine than athletes of individual sports, seeing their athletic performance more affected. Athletes in individual sports felt more able to cope with personal problems than athletes in team sports. Female athletes were significantly more tired and reported more difficulty sleeping than male athletes. CONCLUSION: The situation caused by COVID-19 has had significant effects on the behavior, perception of threat, stress and training patterns of Olympic and Paralympic athletes preparing for the 2020 Tokyo Olympics. It is necessary that sports institutions reinforce mechanisms of help for athletes during future situations of confinement.