Objective Behcet's syndrome (BS) is a chronic, multisystemic and inflammatory syndrome. In our study, we aimed to compare the initiator, effector and inflammatory caspases and pannexin channel protein, which is thought to have an activity in inflammation, in the inflammatory process of BS, with healthy subjects, to investigate their level in patients and their relationship with the clinical findings. Method Forty-six patients who were under follow-up for BS in the Sivas Cumhuriyet University Medical Faculty Department of Internal Diseases, Rheumatology Unit, between January 2017 and June 2017 and 44 healthy controls (HC) who did not have any rheumatic, systemic or metabolic diseases, were enrolled in this study. Results The mean serum pannexin-1 level was 6.36 (4.21-527.2) pg/mL in the BS group and 255.8 (5.38-2000) pg/mL in the HC group. Serum pannexin-1 levels were statistically significantly lower in the BS group (P < 0.0001). The measured mean serum caspase-3 level was 12.04 (11.25-43.69) pg/mL in the group with BS and 12.1 (11.19-484.3) pg/mL in the HC group (P = 0.143), mean serum caspase-9 level was 22 (5.14-29.33) pg/mL in the BS group and 22.01 (11.23-850) pg/mL in the HC group (P = 0.593), mean serum caspase-14 level was 6 (5.2-8.21) pg/mL in the BS group and 6.15 (5.7-353) pg/mL in the HC group (P = 0.053). Conclusion Comparison of serum caspase-3, caspase-9 and caspase-14 levels in subjects with BS and in the HC group did not reveal any statistically significant differences. On the other hand, serum pannexin-1 levels were statistically significantly lower in the BS group.