Two-level hierarchical linear modelling was used to analyse data obtained from TIMSS 1999 database to examine the effect of inquiry-based learning on science achievement of eighth-grade students in Turkey. The influence of teachers' emphasis on scientific reasoning and problem solving and availability of school resources for science instruction on inquiry-based learning and science achievement slopes were also examined. At the student-level, overall plausible values were used as the outcome variable whereas gender, availability of home educational resources, attitude toward science, and inquiry-based learning were predictor variables. At the school level, there were two predictor variables: teachers' emphasis on scientific reasoning and problem solving and availability of school resources for science instruction. While statistically significant and negative relationship was found between inquiry-based learning and within-school science achievement, there were nonsignificant effects of school-level predictors on inquiry-based learning and science achievement slopes.