Aerial parts of Sideritis caesarea H. Duman, Aytaç & Başer are used for complaints such as stomach ache, and intestinal spasm as traditional medicine in Kayseri, Turkey.To investigate the anti-ulcerogenic activity by using bioassay guided fractionation technique (BAGF) and to identify the compound(s) that are responsible for anti-ulcerogenic activity through ethanol-induced anti-ulcerogenic activity model in vivo.Liquid-liquid partition and then different chromatographic techniques were utilized for the BAGF of the ethanol (80%) extract from the aerial parts of Sideritis caesarea. Ethanol-induced gastric ulcer method on rats was employed for the determination of anti-ulcerogenic activity, and ulcer index was calculated for anti-ulcerogenic activity detection.The ethanol (80%) extract of S. caesarea showed potent anti-ulcerogenic activity statistically (95.9% ulcer inhibition, p < 0.001). Among the liquid-liquid fractions, strongest anti-ulcerogenic activity was observed with the ethyl acetate fraction (91.4% inhibition, p < 0.001) and therefore BAGF studies were proceeded with the ethyl acetate fraction. Two anti-ulcerogenic flavonoids {4'-O-methylhypolaetin-7-O-[6‴-O-acetyl-β-D-allopyranosyl-(1 → 2)]-6″-O-acetyl-β-D-glucopyranoside and isoscutellarein-7-O-[6‴-O-acetyl-β-D-allopyranosyl-(1 → 2)]-6″-O-acetyl-β-D-glucopyranoside} were isolated from the ethyl acetate fraction. In addition, a sesquiterpene glycoside [(2E,6E)-2,6,10-trimethyl-2,6,11-dodecatriene-1,10-diol-1-O-β-D-glucopyranoside] and two other flavonoids {4'-O-methylhypolaetin-7-O-[6‴-O-acetyl-β-D-allopyranosyl-(1 → 2)]-β-D-glucopyranoside and isoscutellarein-7-O-[6‴-O-acetyl-β-D-allopyranosyl-(1 → 2)]-β-D-glucopyranoside} were also isolated from the same fraction.Traditional use of S. caesarea in the treatment of stomach-ache were supported by this study and four flavonoids were isolated by using BAGF method and two of them were determined to have significant anti-ulcerogenic activity. Additionally, (2E,6E)-2,6,10-trimethyl-2,6,11-dodecatriene-1,10-diol-1-O-β-D-glucopyranoside was obtained from a Sideritis species for the first time.