Background: Several studies showed that the addition of trunk muscle or core stability exercises in the sport training programs is an effective prevention of spinal and other musculoskeletal injuries. Methods: Twelve female basketball players performed supervised five-week exercise program focused on strengthening the trunk muscles. The program was performed three times per week during pre-season. Sorensen test, Fitnessgram Dynamic Curl-Up test, Prone Plank test and Side Bridge test were used to evaluate trunk muscles performance prior to and immediately after the exercise program completion and again after a three-month follow up period. Results: The results of Sorensen test and Prone Plank test significantly improved immediately after the program, but values returned to baseline at follow-up. In contrast, the results of Fitnessgram Dynamic Curl-Up test and Side Bridge test improved significantly with exercise program and remained significantly higher also at follow-up. Conclusions: Exercise program with emphasis on strengthening the trunk and core muscles can improve muscle performance, however, the results deteriorate shortly after program termination. In order to achieve long-term results, trunk and core muscle exercises have to be performed on regular basis, hence they must be incorporated into general strengthening programs of basketball players.