Background: The purpose was to examine the effects of the type of athletic programme (integrated vs. segregated) on the athletic domain of perceived competence and on general self-worth. Methods: Participants were 32 adolescent females with intellectual disabilities (ID), divided equally into four groups: (1) segregated swimming; (2) integrated swimming; (3) adapted physical activity; and (4) sedentary. The experimental treatment was 32 months long; for sport groups, this involved 2 h of training each week and 12 competitive meets. The Harter Self-Perception Profile for Children 11 times was administrated to determine changes in perceived physical competence and general self-worth. Results: Results indicated (1) no change in perceived general self-worth for the four groups; (2) significantly lower perceived athletic competence only for the integrated swimming group, despite the increase in athletic performance. Conclusions: The integrated sport participation for adolescents with ID placed in segregated school is useful but needs to be well controlled by professional in physical education.