This study is about the influence of gender on the participation of boys and girls in science subjects in co-educational secondary schools in Uganda. Evidence from the study shows that the teaching and learning that goes on in many co-educational classrooms often promotes inequitable participation of boys and girls. In such classrooms, girls tend to be more passive than boys in science classes, leading to girl’s lower performance, especially in physics and chemistry. This points to gendered classroom configurations and confirms the argument that in co-educational science classrooms, girls still constitute ‘students at risk’. This raises the concern for equity and begs for the need to establish support-systems for girls in order to build their self confidence in sciences. This in turn calls for the streamlining of gender concerns into both educational theory and practice.