Background and Objectives: Health status during adolescence may predetermine that during adulthood. Being short because of nutritional and health adversity, where stunting is indicative, is a global health concern, possibly in adolescence. This study assessed the prevalence of shortness (defined by HAZ ＜-2 SD) at age 12 and its determinants. Study Design: This Tanjungsari birth cohort of 1988/1989 was revisited in 2001-2002 with 3093 participating children, their parents and households. The cohort was tracked from birth, to ages 2 and 12 with anthropometry, with birth weight, then weight and height-for-age at 2 and 12, dietary history at age 2, health patterns at age 2 and 12, and environmental exposures. Results: The prevalence of adolescent shortness, presumed 'stunting', was 48.8% for which predictor Odds Ratios (OR) were low birth weight 1.64 (95% CI: 1.28-2.09), short height for age at 2-years 1.54 (95% CI: 1.33-1.80), limited maternal education 1.19 (95% CI: 1.01-1.41), unimproved source of drinking water 1.27 (95% CI: 1.08-1.49), unimproved latrine 1.18 (95% CI: 1.01-1.39) and presence of atopic disease at 12 years of age 1.29 (95% CI: 1.01-1.65). Smoking exposure, not breastfed, formula milk consumption and infectious disease at age 2 were not associated with shortness at age 12 on multivariable analysis. Conclusions: Adolescent shortness was found in almost half of this rural Javanese cohort followed from birth. It was associated with birth weight, and several individual, maternal and environmental factors evident at age 2, along with an atopic disposition at age 12. However, stature itself may not constitute a health risk over and above the associated socio-environmental conditions.