The OECD's Programme for International Student Assessment (PISA) enables participating countries to monitor 15-year old students' progress in reading, mathematics, and science literacy. The present study investigates persistent factors that contribute to science performance of Turkish students in PISA 2006 and PISA 2009. Additionally, the study investigates whether factors explaining science performance has changed between 2006 and 2009. Multilevel analyses of student level and school-level variables revealed that the variance in science performance explained by school-level variables is 13 % for PISA 2006 and 28 % for PISA 2009. Moreover, the variance in science performance explained by student-level variables is 19 % for PISA 2006 and 20 % for PISA 2009. The six most common student-level variables in PISA 2006 and 2009 were statistically significant predictors of science performance. At the school level, location of school was a significant predictor of science achievement in both PISA 2006 and 2009.