This study concerns the assessment of the effects of Index of Principals' Perception of School Climate (PPSC), intimidation of students and gender in Moroccan public schools on student performance in science. The study focused on fourth grade students who participated in the TIMSS 2007. The objective of this study is to answer the following research questions: (1) Do schools make a difference in science achievement? (2) What is the effect of the index of principals' perception of school climate (PPSC) on student achievement? (3) What is the impact of intimidation by other students and gender on student achievement? What is the difference between urban and rural schools in science achievement? The results of the multilevel analysis show that the total variance situated at the school level is 24% in urban school, 50% in rural school and 42% in urban and rural together. Also, they affirm as the intimidation penalizes students' performances in sciences, the PPSC index is negatively correlated with the students' performances and the urban schools are favored compared to those in the rural areas.