Background: Tobacco use is a major preventable cause of death in the world. This article describes and compares tobacco use prevalence for students attending junior high schools and senior high schools in Taiwan. Methods: This report uses data from the Global Youth Tobacco Survey (GYTS) completed among 4689 junior high school students and 4426 senior high school students in Taiwan in 2004-2005. The GYTS uses a 2-stage sampling design to produce nationally representative data for junior and senior high students in general and vocational schools. Results: Higher smoking prevalence was observed among senior high (10.1% general schools and 15.9% vocational schools) than junior high (5.5%) school students. Smoking prevalence of girls in junior high (3.2%) and senior high schools (4.6% general and 11.1% vocational) was almost as high or higher than adult females' (4.3%) smoking rates. The pattern of smoking intensity across school years and type of school shows that the percentage of smokers who were experimenters (47.1%) was higher in junior high school and the percentage of smokers who were regular/established smokers (over 50%) was higher in senior high school. Conclusions: Smoking prevalence described in this report shows that there are challenges facing the tobacco prevention and control program in Taiwan. The findings suggest that schools should increase their smoking initiation prevention efforts and make available cessation programs and counseling to help students quit smoking. If effective youth tobacco control programs are not developed and implemented in Taiwan, future morbidity and mortality attributed to tobacco will surely increase, especially among women. (Contains 3 tables and 1 figure.)