The purpose of this study was to estimate the prevalence of children aged 0-6 years with developmental delay (DD) and to examine age-period trends in the prevalence of DD diagnosis in Taiwan. For the study population, we selected children aged <6 years at baseline (in 1997-2002, N=2,308,790) from the National Health Insurance Research Database (a longitudinal database with annual medical records of children in Taiwan) to estimate the prevalence of DD. All study subjects were followed up until they were 5 years old; the study period was from 1997 to 2008. The prevalence of DD by year gradually increased from 0.16% to 3.25% from 1997 to 2008 with an increasing ratio of prevalence of 20% over the 12-year study period. The prevalence of DD in boys was 2.13 times (2.09-2.18 from 1997 to 2008) that in girls. The prevalence of DD increased by year of study. The effect of sex on the prevalence of DD was significant. Understanding the trend of prevalence in the study period and the gap between the rate of early treatment and DD prevalence are critical concerns for future research.