Atherosclerosis in patients with type 2 diabetes is characterized by endothelial dysfunction associated with impaired flow-mediated dilatation (FMD) and increases retrograde and oscillatory shear. The present study investigated endothelium-dependent vasodilatation and shear rate in patients with type 2 diabetes at baseline and follow-up after 12 weeks of low-volume high-intensity interval training (LV-HIIT) or continuous moderate-intensity training (CMIT). Seventy-five sedentary patients with type 2 diabetes and untreated pre- or stage I hypertension were randomly divided into LV-HIIT, CMIT and control groups. The LV-HIIT group intervention was 12 intervals of 1.5 min at 85-90% maximal heart rate (HR ) and 2 min at 55-60% HR . The CMIT group intervention was 42 min of exercise at 70% HR for three sessions per week during 12 weeks. High-resolution Doppler ultrasound was used to measure FMD, arterial diameter, anterograde and retrograde blood flow, and shear rate patterns. Brachial artery FMD increased significantly in the LV-HIIT group (3.83 ± 1.13 baseline, 7.39 ± 3.6% follow-up), whereas there was no significant increase in the CMIT group (3.45 ± 0.97 baseline, 4.81 ± 2.36% follow-up) compared to the control group (3.16 ± 0.78 baseline, 4.04 ± 1.28% follow-up) (P < 0.05). Retrograde shear in the LV-HIIT group decreased significantly (P < 0.05), and no significant decrease in retrograde shear was seen in the CMIT group. Anterograde shear after LV-HIIT increased significantly (P < 0.05) but was unchanged in the CMIT group. However, oscillatory shear index in both exercise groups decreased significantly (P = 0.029). Nitrite/nitrate (NOx) level increased in both exercise groups, but the increase was greater in the LV-HIIT group (P < 0.001). The results indicate that by increasing NOx, HIIT decreases the oscillatory shear-induced improvement in FMD and outward artery remodelling in patients with type 2 diabetes.