OBJECTIVE: The aim of this study was to compare the effect of a short-term intensive residential yoga program with physical exercise (control) on pain and spinal flexibility in subjects with chronic low-back pain (CLBP). DESIGN: This was a wait-list, randomized controlled study. SETTING: The study was conducted at a residential integrative health center in Bangalore, South India. SUBJECTS: Eighty (80) subjects (females, n = 37) with CLBP, who consented were randomly assigned to receive yoga or physical exercise if they satisfied the selection criteria. INTERVENTION: The intervention consisted of a 1-week intensive residential yoga program comprised of asanas (physical postures) designed for back pain, pranayamas (breathing practices), meditation, and didactic and interactive sessions on philosophical concepts of yoga. The control group practiced physical exercises under a trained physiatrist and also had didactic and interactive sessions on lifestyle change. Both of the groups were matched for time on intervention and attention. OUTCOME MEASURES: Pain-related outcomes were assessed by the Oswestry Disability Index (ODI) and by spinal flexibility, which was assessed using goniometer at pre and post intervention. Data were analyzed using repeated measures analysis of variance (RMANOVA). RESULTS: Data conformed to a Gaussian distribution. There was a significant reduction in ODI scores in the yoga group compared to the control group (p = 0.01; effect size 1.264). Spinal flexibility measures improved significantly in both groups but the yoga group had greater improvement as compared to controls on spinal flexion (p = 0.008; effect size 0.146), spinal extension (p = 0.002; effect size 0.251), right lateral flexion (p = 0.059; effect size 0.006); and left lateral flexion (p = 0.006; effect size 0.171). CONCLUSIONS: Seven (7) days of a residential intensive yoga-based lifestyle program reduced pain-related disability and improved spinal flexibility in patients with CLBP better than a physical exercise regimen.