The purpose of this paper is to examine the characteristics of Albanian secondary schools, which are associated with reading achievement and the effects of gender and socio-economic status on reading performance of 15-year-old students. This study used data on the background and achievement of 4,596 students in 181 Albanian schools from the 2009 Programme for International Student Assessment (PISA). Given the nested structure of the data, two-level Hierarchical Linear Modeling (HLM) methods were used to address multilevel research questions. About a third of the total variance in reading performance lies between schools, indicating that school characteristics are important in predicting student achievement. The results clearly reveal the significant relationships of socio-economic status (SES) and gender with student achievement, even after controlling for family structure (two parent families versus others), learning strategies use, and reading engagement. There is also a substantial variability among schools on gender difference in student performance and the effect of SES on student performance. The results from the between-school model suggest that school type, school SES and classroom environment are significant predictors of school performance. Moreover, gender gap in reading performance is associated with school sector (public/private), school location (urban/rural), and average reading engagement; and SES effect on student performance is associated with school type (general/vocational), school location and average reading engagement. The characteristics of schools that make them excellent and more equitable are summarized.