One argument for the inclusion of children with special education needs (SEN) is that they will benefit from the interactions and relationships with their typically developing peers. However, students with SEN tend to be more rejected than their non-SEN peers. Considering the negative consequences of peer rejection on socioemotional development and school adjustment, the current study aims to understand the behavioural correlates and specific characteristics of the students with SEN associated with peer rejection. Participants were 227 students (107 with SEN); 53.7% male; mean age 10.79 (SD = 2.16); attending the 3rd (33.9%), 5th (35.3%) and 7th grades (30.8%). Students filled in a Sociometric task and 47 regular school teachers and 31 special education teachers provided information regarding sociodemographic and educational data, behavioural characteristics and student-teacher relationship. SEN status was the most important predictor of rejection followed by social skills. In the case of students with SEN, less familiarity with peers and a less close student-teacher relationship were also associated with rejection. Thus, the findings emphasise the need of professional development programs to assist teachers in the promotion of positive relationships with their students and a positive peer culture within the class.