Pilates programs are widely used as a form of regular exercise in a broad range of populations investigating their effectiveness for chronic low back pain (CLBP) treatment. The aim of this study was to compare the effects of a Pilates program and a trunk strengthening exercise program on functional disability and health-related quality of life (HRQOL) in women with nonspecific CLBP. A total of 101 volunteer women with CLBP provided data with a 3-month follow-up. They were randomized to either a Pilates (n= 37), trunk strengthening exercise (n= 36) or a control group (n= 28), exercising for a period of 8 weeks, three times a week. Data were collected on HRQOL using the Short-Form 36 Health Survey (SF-36v2), and functional disability using the Roland Morris Disability Questionnaire prior to program initiation, mid-intervention, immediately after program termination, and three months post-intervention. The Pilates participants reported greater improvements on self-reported functional disability and HRQOL compared with participants in the trunk strengthening exercise and control groups (p < 0.05). The effects were retained for a period of three months after program termination for the Pilates group and to a lesser extent for the trunk strengthening exercise group. An 8-week Pilates program improved HRQOL and reduced functional disability more than either a trunk strengthening exercise program or controls among women with CLBP.