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Introduction: Polycystic Ovarian Syndrome (PCOS) is an endocrine disorder, and individuals with this condition are at a risk of developing complications like metabolic syndromes throughout their lifetime. Not much is known about studies reporting the combined effects of calisthenic exercise with either aerobic exercise or progressive resistive exercises that have shown positive outcomes in PCOS. Need for the study: Extensive literature search has revealed gaps in reporting the individualised effects of calisthenic exercise in PCOS and its comparative effects with yoga. The present research article presents a study protocol comparing calisthenic exercises and yoga protocols prescribed for women with PCOS. Aim of the study: To evaluate and compare the effects of calisthenic exercises and yoga in women with PCOS. Materials and Methods: This research protocol is planned to conduct a randomised clinical trial in Belagavi, Karnataka, India, and will employ a randomised, open-label, parallel-armed, double-blinded clinical experimental design. The duration of the study will be near bout four years, from June 2022 to August 2026. A total of 102 females with PCOS, aged between 18 and 35, will be randomly allocated to either a yoga group (N=51) or a calisthenic exercise group (N=51). For a period of 1½ months (i.e., six weeks), group therapy sessions will be held five times a week. Ultrasonography scans, which will assess ovarian cyst count and size, ovarian volume, and total lipid profile, will be conducted twice (pre- and post-intervention). The PCOS Questionnaire (PCOSQ-26) will be utilised to assess health-related quality of life, as well as anthropometric measurements such as waist-hip ratio and Body Mass Index (BMI). These measurements will be assessed prior to the intervention, six weeks following the intervention, and at the 12-week follow-up. Inferential as well as statistical methods will be used to analyse the gathered data. A test for normal distribution will be conducted, depending on whether parametric tests (Z test and/ or ANOVA) or non-parametric tests (Mann-Whitney U test or Wilcoxon signed-rank test) will be performed. A probability value of less than 0.05 will be considered statistically significant. [ABSTRACT FROM AUTHOR]