Much research into school effectiveness fails to distinguish between pupil and classroom or teacher effects on the one hand, and ' ‘real’ school effects on the other. Moreover Dutch research into effective secondary schools is primarily concerned with pupil attainment whereas most Anglo-Saxon literature on this topic deals with pupil cognitive achievement. In this article an attempt is made to contribute to these topics by using a large scale Dutch data set on pupil achievement in secondary education. After a short descriptive paragraph on pupil achievement in Dutch secondary education, a multilevel instructional and school effects model of pupil achievement is developed and tested. The results show that it is hard to distinguish instructional and teacher effects from school effects and that there are complicated cross-level interaction effects on achievement. For some pupils, instructional factors are more important than for others; some instructional features only play a significant role in specifically organized schools.