Background: Aerobic exercise and specifically high intensity interval training (HIIT) has been established to improve the vascular function in a range of clinical conditions (Ramos et al., 2015). HIIT has demonstrated a strong microangiopathic element which has shown that clinical outcomes in those conditions benefit from exercise. However, the effect of HIIT on microcirculation in systemic sclerosis (SSc) patients has yet to be investigated. Therefore, the purpose of the study was to examine whether a HIIT protocol on a cycle or on an arm crank ergometer could improve the microcirculation in the digital area in SSc patients. Methods: Thirty three SSc patients (65.3 ± 11.6 years old) were randomly allocated in three groups (cycling, arm cranking and control group). The exercise groups underwent a twelve-week exercise program twice per week. All the patients performed the baseline and post-exercise intervention measurements where the physical fitness, functional ability, transcutaneous oxygen tension (ΔtcpO2), body composition and quality of life were assessed. Endothelial-dependent and independent-vasodilation were assessed in the middle and index fingers using LDF and incremental doses of acetylcholine (Ach) and sodium nitroprusside (SNP). Cutaneous flux data were expressed as cutaneous vascular conductance (CVC). The present study was approved by the Health Research Authority of the National Health System and conducted according to the Helsinki Declaration. An informed consent was obtained from all participants. Results: Peak oxygen uptake increased in both exercise groups (p<0.01, d=1.36). ΔtcpO2 demonstrated an increase only in the arm cranking group, with a large effect size but not statistically significant (p=0.59, d=0.93). Endothelial-dependent vasodilation improved in the arm cranking (p<0.05, d=1.07) compared to other groups. Endothelial-independent vasodilation did not show any significant change. Both exercise groups improved life satisfaction (p<0.000) as well as discomfort and pain of Raynaud’s phenomenon (p<0.05). Arm cranking seems to be the preferred mode of exercise for the twelve-week exercise program compared to cycling (p<0.05). No changes were observed in the body composition or the functional ability between the groups. Conclusion: Our results suggest that the arm cranking has the potential to improve the microvascular endothelial function in SSc patients. It is also noteworthy to say that the training dose of the twelve-week HIIT program, twice per week, revealed to be a sufficient and tolerable dose-response for this population. Future research should focus on exploring more exercise elements such as the combination of aerobic and resistance training on a vascular and molecular level as well as the quality of life in SSc patients.