A total of 128 patients (86 CM, middle age 44.8±11.2; 42 EM, 49.2±12.2) were recruited. In the univariate analysis, CGRP, VIP and PACAP were higher in CM vs EM (p<0.001). The multinomial regression model could only correctly predict 60.2% of CM, 68.8% of EM and 15.5% of healthy controls. Only VIP (B=0.009; p=0.012) and PACAP (B=0.003, p=0.002) predicted CM diagnosis, but not EM. CGRP did not predict CM or EM. Individually, CGRP was the best to classify CM (65%) and PACAP for EM (88.5%). Neuropeptide levels correlated with MIDAS. Only PACAP correlated with total headache days (p=0.002). Neuropeptide levels were higher in patients under BT. CGRP and VIP did not differentiate AOP from NT, but PACAP did (higher in AOP than in NT; p <0.001). In the sensitivity(Se) – specificity(Sp) analysis, Sp was low for all of them as CM biomarkers (VIP:Se=0.77, Sp=0.43; PACAP:Se=1, Sp= 0.53 ; CGRP:Se=0.60, Sp=0.445).