Low-intensity training at long muscle-tendon unit lengths with a greater passive force may cause muscle swelling, which may be related to hypertrophy, even if the active force production is lower than that at short muscle-tendon unit lengths. This study compared muscle swelling after low-intensity torque-matched isometric exercises at long and short muscle-tendon unit lengths. Twenty-six volunteers performed isometric knee flexion exercises (30% of maximal voluntary contraction× 5 seconds×10 repetitions×9 sets) either at long or short lengths of the hamstrings (90° hip flexion and 30° knee flexion, or 90° hip and knee flexion, respectively). Active torque was calculated by subtracting passive torque from the total torque generated during exercise. Swelling-induced changes in cross-sectional area was assessed before and after exercise using ultrasonography. There was no between-group difference in the total torque during exercise; however, the active torque was significantly lower in the group trained at long than in the group trained at short muscle-tendon unit lengths. Muscle swelling occurred in both groups. The results suggest that exercise at long muscle-tendon unit lengths can cause similar muscle swelling as exercise at short muscle-tendon unit lengths, even in cases where active torque production is lower than that at short lengths.