Background: Evidence on the prevalence and associated factors of anemia among young adolescent girls and boys in rural western China is limited. Methods: We used data from a follow-up study of adolescents (10-14 years) born to women who participated in a randomized trial of antenatal micronutrient supplementation in western China. Anemia was defined by World Health Organization standards. Logistic regression was used to examine the risk factors for anemia. Results: The overall prevalence of anemia was 11.7% (178/1517). Female adolescents were 1.73 (95% CI 1.21, 2.48) times more likely to have anemia as compared to males. Adolescents whose mothers had completed high school were 65% (95% CI 7%, 87%) less likely to be anemic, compared with those of whom had <3 years. Household wealth was also inversely associated with anemia. The association of puberty status with anemia was modified by adolescent sex (p-value for interaction was 0.04): males with greater than mild puberty development had 65% (95% CI 17%, 85%) reduced odds of anemia while there was no association among females (OR: 0.72, 95% CI 0.29, 1.78). Consumption of flesh foods, eggs, and having a meal frequency of three times or more per day were associated with 42% (95% CI 11%, 62%), 40% (95% CI 7%, 62%) and 32% (95% CI 4%, 52%) reduced odds of anemia, respectively. Conclusions: Anemia is a public health problem among adolescents in rural western China. Nutritional and social determinants were identified as predictors, warranting interventions to reduce the risk of anemia among this critical age group.