Background: Yoga exercises are often used as a form of body and mind exercise to increase performance. However, knowledge about the physiologic effects of performing high-intensity Hatha yoga exercises over a longer time period remains limited. Objective: To investigate the effects of high-intensity yoga (HIY) on cardiovascular fitness (maximal oxygen consumption, estimated from the Cooper running test), ratings of perceived exertion (RPE), heart rate (HR), heart rate recovery (HRR), blood pressure (BP), adipocytokines, apolipoprotein A1 (ApoA1), apolipoprotein B (ApoB), and glycosylated hemoglobin (HbA1c) in healthy students. Methods: The 44 participants (38 women and 6 men; median age, 25 years [range, 20-39 years]) were randomly assigned to an HIY or a control group. The HIY program was held for 6 weeks (60 minutes once a week). Cardiovascular fitness, RPE, HR, HRR, BP, adipocytokines, HbA1c, ApoA1, and ApoB were measured at baseline and after 6 weeks in both groups. Results: HIY had no significant effects on cardiovascular fitness (mean dose: 390 minutes [range, 210-800 minutes]), HR, HRR, BP, or any of the blood parameters. However, ApoA1 (1.47 -0.17 to 1.55 -0.16 g/L; p = 0.03) and adiponectin (8.32 -3.32 to 9.68 -3.83 mg/L; p = 0.003) levels increased significantly in the HIY group after 6 weeks. Conclusions: Six weeks of HIY did not significantly improve cardiovascular fitness. However, ApoA1 and adiponectin levels increased significantly in the HIY group. This finding suggests that HIY may have positive effects on blood lipids and an anti-inflammatory effect.