The present study aimed at researching whether students with formally diagnosed behavioural, emotional and social difficulties (BESD) differ in their self-perceived emotional and social inclusion as well as in their academic self-concept, depending on individual behavioural pattern (externalising and internalising behaviour) and school setting (inclusive and special education). In order to examine these research issues, students with diagnosed BESD from grade five to eight in inclusive and special school classes in Germany, North-Rhine Westphalia were questioned about their school-linked self-perceptions. Two-way analyses of variance were applied in order to investigate the relations between the included variables. The results indicate that academic self-concept of students with BESD is significantly more positive in special education than in inclusive education. Self-perceived social inclusion and academic self-concept of students with internalising behaviour prove to be significantly more negative in comparison to students with externalising behaviour. Descriptive statistics indicate that especially students with internalising behaviour in inclusive education are affected by low self-perceptions in school.