The purpose of this study was to compare the effect of High Intensity Interval Training (HIIT) versus Aerobic Exercise (A-Ex) following 12 wks of training. Twenty-one Sprague Dawley rats (11 to 13 months) were assigned to 3 groups: (1) Control Group (no exercise); (2) A-Ex Group; and (3) HIIT Group. The A-Ex Group was submitted to treadmill exercise at a speed of 20 m·min-1 with a rest period of 90 sec every 5 min for 20 min 5 d·wk-1. The HIIT Group was submitted to treadmill exercise at a speed of 35 m·min-1 with a rest period of 90 sec every 5 min for 15 min 5 d·wk-1. At weeks 4 and 12, relative Leukocyte Telomere Length (LTL) was compared to week 4 of the Control Group using q-RT-PCR. It was shown that relative LTL in the A-Ex Group at week 4 and 12 was significantly longer compared to week 4 of the Control Group (P < 0.05), but no significant difference in the HIIT Group compared to the Control Group (P > 0.05). We concluded that 12 wks of aerobic and HIIT exercise both cause lengthening of relative LTL. Aerobic exercise has a better effect compared to HIIT in relation to changes in relative LTL. © American Society of Exercise Physiologists.