BackgroundAdolescence is last chance for curbing the consequences of malnutrition and breaking the intergenerational cycle of malnutrition and poor health. This study aimed to assess the prevalence and the factors associated with stunting and thinness among in-school adolescents in northern Ethiopia using the 2006 World Health Organization (WHO) standards.MethodsIn-school adolescents (n = 348, 10–19 years old) were randomly selected to participate in this cross-sectional study. Anthropometric measurements were carried out to determine the proportion of adolescents who were stunted (height-for-age < −2 Standard Deviation (SD)) and thin (body-mass-index-for-age < −2 SD). T-test was employed to evaluate mean weight and height differences between groups. Pearson chi-square, chi-square trend and Fisher’s exact tests were used to explore the crude association of categorical outcome variables and associated factors. Crude and adjusted associations between the outcome variables (stunting and thinness) and independent variables (socio-demographic, eating behavior and sanitation) were also determined using logistic regression. Stata version 11.1 was used to analyze the data.ResultsThe height of the adolescents was 147.6 ± 11.2 cm (mean ± SD) and weight was37.2 ± 9.5 kg. The mean Z-scores of height-for-age and body-mass-index (BMI)-for-age of adolescents were −1.49 and −1.29, respectively. The prevalence of stunting and thinness among adolescents was 28.5 % (boys = 37.7 %; girls = 21.2 %; P = 0.001) and 26.1 % (boys = 32.4; girls = 21.6 %; p = 0.017), respectively. Adolescents in 13–15 year old age group (Adjusted Odds ratio (AOR) = 2.23; 95 % CI: 1.22, 4.08), boys (AOR = 2.53; 95 % CI: 1.52, 4.21) and rural residents (AOR = 2.15; 95 % CI: 1.20, 3.86) had significantly higher odds of being stunted compared to their counterparts. Furthermore, boys had higher (AOR = 1.97; 95 % CI: 1.19, 3.25) odds of being thin compared to girls. Compared to those 10 to 12 years of age, adolescents in 16 to 19 years of age were 53 % (AOR = 0.47; 95 % CI: 0.23, 0.95) less likely to be thin.ConclusionsUndernutrition is widely prevalent among adolescents in northern Ethiopia. Sex, age and area of residence significantly associated with adolescent undernutrition. The study underlines the need for nutrition interventions targeting rural and boy adolescents.