Introduction: Between-class ability grouping practice in Malaysian Secondary Schools was studied in order to find the influence students' perception on their teachers' behavior on their self-esteem. Students' perception on teachers' behaviors were divided into two categories: controlling students' behavior to avoid disciplinary matters and supporting students' academic achievements. Method: 302 students from four public secondary schools were selected to participate in this study. Self-esteem levels of the students were measured using the Rosenberg Self-Esteem Scale. All scales were translated into local language and internal consistency reliability scores. Mean and t-test were used to analyze the difference of self-esteem between two groups as well as the difference of students' perception on teachers' behavior between two groups. For analyzing the mentioned differences within groups, mean and paired t-test were used. Influence of students' perceptions on teachers' behavior on students' self-esteem were analysed with multiple regression. Results: Results showed that students from high achievers' groups scored significantly higher in self-esteem compared to the students from low achievers' groups. A significant difference in perception on teachers' behavior between the students in the high and low achievers' groups was found; students from high-achievers' groups perceived their teachers to be more supportive while the other groups perceived their teachers to be more controlling. Amongst high-achievers groups, self-esteem were significantly influenced by perception on teachers', supporting behavior, while amongst low-achievers' groups, self-esteem were significantly influenced by perception on teachers' controlling behavior. Discussion or Conclusion: It is indicated that teachers might have different preconceived idea on the students based on their classrooms assignment. This difference is visible through their overt behavior, which was then perceived by the students, and in turn, influences the students' self-esteem. (Contains 8 tables.)