Background: Adolescents girls were given little health and nutrition attention. Focusing on adolescent girls' nutrition prior to conception is one way to break the intergenerational cycle of malnutrition. Therefore, the aim of this study was to assess the prevalence of undernutrition and associated factors among adolescent girls in rural Damot Sore District, Southern Ethiopia. Methods: A community based cross-sectional study was conducted from February to March, 2017. Multistage sampling technique was used to select 729 adolescent girls. Structured interviewer administered questionnaire was used to collect information on different variables. Weight and height were measured by well-calibrated digital Seca scale and portable stadio-meter by trained data collectors. Descriptive statistics, bivariable and multivariable logistic regression analysis was done. Strength of association of dependent and independent variables was presented by odds ratio along with its 95% CI. Results: The prevalence of stunting and thinness among adolescent girls were 29.6% (95% CI= 26.6%, 32.8%) and 19.5% (95% CI= 16.7%, 22.3%) respectively. Being in older adolescence period (AOR= 2.06, 95%CI= 1.08, 3.92), mother occupation (farmer and government employee) [(AOR= 2.38, 95%CI= 1.31, 4.33) and (AOR= 3.05, 95%CI=1.35, 6.92)], mother education (secondary and more than secondary) [(AOR= 0.53, 95%CI= 0.28, 0.98) and (AOR= 0.25, 95%CI= 0.09, 0.69)] and household wealth index (poor) (AOR= 1.94, 95%CI= 1.29, 2.92) were significantly associated with stunting. Father education (primary and secondary) [(AOR= 0.48, 95%CI= 0.31, 0.77) and (AOR= 0.45, 95%CI= 0.26, 0.78)], mother education (primary) (AOR=0.56, 95%CI= 0.37, 0.87) and meal frequency (<2/day) (AOR= 1.87, 95%CI= 1.12, 3.13) were significantly associated with thinness. Conclusion: High prevalence of stunting and thinness were observed in the study area. In older adolescence, from poor family, mother occupation and eating less meal per day were negatively associated while educated both parents was positively associated with stunting and thinness. Initiation of routine screening and implementing evidence based community nutrition programmes is needed to improve nutritional status of adolescent girls.