Background: Since the early 1980s there have been extensive federal, state, and local efforts to improve schools for all students, including broad policy initiatives intended to change the school experiences of students with disabilities. These efforts have had significant impacts on policy and practice at all levels of the education system, including a renewed focus on academics, evidence-based interventions, and achievement testing. Two studies sponsored by the U.S. Department of Education provide documentation of changes experienced since the mid 1980s by secondary school students with disabilities. Purpose: To examine the extent and direction of change in the school experiences (e.g. school characteristics, courses, instructional settings, attendance, grades) of students with disabilities in middle and high school in 1986 and 2002. Study Sample: The National Longitudinal Transition Study (NLTS) included a nationally representative sample of 14,000 youth receiving special education, ages 15 through 23 in the 1985-86 school year. The National Longitudinal Transition Study-2 (NLTS2) includes a nationally representative sample of 11,276 youth who were ages 13 through 16 and receiving special education services in seventh grade or above in the 2000-2001 school year. Comparative analyses include the age group of students for which school data were collected in Wave 1 of both studies: 14-through 18-year-olds. All statistics from the studies are weighted estimates of the national population of students receiving special education in the studies' age ranges at the time of the studies, as well as of each disability category individually. Research Design: Descriptive; Correlational; Longitudinal; Other Quantitative. Data Collection and Analysis: NLTS2 information reported here is drawn from the first wave of school surveys and school record abstracts conducted for each student's most recent year in school, either the 1985-86 or 1986-87 school year. For NLTS2 students data are drawn from two mail surveys that were conducted with school staff in the spring of the 2001-02 school year. Findings: By 2002 there were significant changes in youth with disabilities' school programs. High school students with disabilities were more likely to be taking core academic classes, more likely to be taking those courses in general education classes, less likely to be taking any special education classes, and less likely to be taking vocational courses. There was an increase in the average number of days absent for students with disabilities and an increase in the rate of suspensions. There was a shift from students receiving mostly Cs to more students receiving mostly As or Bs. There were differential changes in school experiences for youth who differed in their disability category, grade-level, household income, or race/ethnicity. Conclusion: The differences over time between groups of students with disabilities in their school experiences raise the question of whether there may be related differences in postschool outcomes. Comparisons of findings from the second wave of data collection of NLTS and NLTS2 will examine their achievements in the early years after high school. Citation: Wagner, M., Newman, L., & Cameto, R. (2004). Changes over time in the secondary school programs of students with disabilities. A report of findings from the National Longitudinal Transition Study and the National Longitudinal Transition Study-2 (NLTS2). Menlo Park, CA: SRI International. (Contains 58 exhibits and 2 footnotes.)