Introduction: Behcet's disease (BD) is a chronic inflammatory disease which can be limited to only mucocutaneous tissues or can affect different systems of the body. Aim: To investigate the association of endothelial and erectile dysfunctions with BD, on the basis of comparative analysis between mucocutaneous and systemic BD. Material and methods: Thirty-eight men diagnosed with BD were included in the present study. The patients were stratified into two groups as mucocutaneous BD (n = 20, MBD group), and systemic BD (n = 18, SBD group). Erectile dysfunction (ED) was assessed using the Erectile Function domain of the International Index of Erectile Function (IIEF-EF) questionnaire. The coronary flow reserve (CFR) assessment was done for analysing endothelial dysfunction (EnD), and CFR < 2 was defined as EnD. Penile Doppler ultrasonography (PDU) was performed for ED. The demographic and clinical parameters, IIEF-EF score ED classification, CFR and PDU test findings were compared between two groups. Results: The median age was 34 (22-52) years in the overall population, and there was no difference between two groups (p = 0.558). Time from diagnosis was significantly longer (24 vs. 102 months, p = 0.021) and the use of immunosuppressive therapies was higher (0 vs. 70.6%, p < 0.001) in the SBD group. In overall, median CFR was 1.92 (1.1-5.96), and there was no difference between two groups (1.88 vs. 1.97, p = 0.812). The percentage of patients with CFR < 2 was similar in two groups (52.6% vs. 52.9%, p = 0.985). The ED status according to IIEF-EF was similar in two groups (45% vs. 27.8%, p = 0.538) as well as according to PDU analyses (10% vs. 16.7%, p = 0.544). Conclusions: The increased risk of endothelial, and erectile dysfunctions should be considered in men who were diagnosed with mucocutaneous and systemic BD.