The study investigates the effects of certain school characteristics on students’ mathematics performances in Turkey in the PISA 2006 while controlling for family background and demographic characteristics. Three models of Hierarchical Linear Modeling (HLM) are constructed. The results reveal that 55% of the variance is attributable to between-schools and the remaining 45% to individual student characteristics. About two-thirds of the 55% is explained by selectivity in admissions, time to study mathematics and students’ SES, gender and the geographical region. The findings are interpreted to explain why Turkish schools differed greatly in average student performance in PISA 2006 by using the conceptual efforts on school quality factors and family background characteristics.