Background and Purpose: Pilates mat and Swiss Ball exercise are complementary alternative medicine (CAM) therapies currently utilized as preventative health and fitness measures as well as methods of rehabilitation. Minimal evidence based information exists regarding the efficacy of most CAM therapies. The purpose of this study was to compare the effects of Pilates mat and Swiss ball exercise training upon trunk endurance and lower extremity strength of older healthy females. Subjects: One hundred eleven women were randomly assigned to Pilates mat, Swiss ball and control groups. Methods: Subjects participated in 10 weekly of biweekly exercise training. Outcome measures included assessment of trunk endurance (trunk flexion and extension) and lower extremity (gluteus medius and quadriceps) strength via hand-held dynamometry. Results: Eighty-three subjects completed the study. Both Pilates mat and Swiss ball participants exhibited statistically significant improvement in rectus abdominus endurance. Initial ANOVA results for pre/post rectus abdominus endurance deltas among Pilates. Swiss and control groups was p=.03, but post-hoc Tukey’s tests indicated that only the rectus abdominus endurance changes between Swiss ball and control participants differed. A subsequent ANOVA of only beginner (deconditioned) fitness level participants results for pre/post rectus abdominus endurance deltas among Pilates, Swiss and control groups was p= .02 and post-hoc Tukey’s indicated that only the rectus abdominus endurance changes between Pilates and control group participants differed. Swiss ball participants exhibited statistically significant improvement in trunk extensor endurance. Initial ANOVA results for pre/post trunk extensor endurance deltas among Pilates, Swiss and control groups was p=.04 and post-hoc Tukey’s tests indicated that the only trunk extensor endurance changes between Swiss ball and control group participants differed. No statistically significant improvement in lower extremity strength was observed in either Pilates mat or Swiss ball participants. Discussion and Conclusion: The results suggest that Pilates mat and Swiss ball exercise participation effectively improve trunk endurance in healthy older females.