The standardized International Study of Asthma and Allergies in Childhood (ISAAC) is a valid tool in assessing prevalence of asthma indices. In order to determine the time trends of childhood asthma in Taiwan, we compared data from nationwide ISAAC surveys from a very large sample of Taiwanese 12- to 15-year-old school children, using ISAAC core written and video questionnaires. The number of participants was 44,104 in 1995–96 (phase I) and 11,048 in 2001 (phase III). We found a general tendency towards an increase in lifetime prevalence of physician-diagnosed asthma and asthma symptoms between two surveys, more marked for girls than for boys. Most of the 12-month prevalence of asthma symptoms decreased among boys but stabilized among girls. When comparing different severity levels, we also noted that the decreasing trends of current symptoms were more marked with regard to severe symptoms than mild symptoms in both sexes. A combination of both improved awareness and management of asthma might in part explain this circumstance. Over the past decade in Taiwan, the lifetime prevalence of childhood asthma was increasing, more marked among girls; however, the 12-month prevalence of asthma symptoms was decreasing, mostly among boys. The exact reasons for such trends remain to be explored.