The present study investigates differentiation in content and language integrated learning (CLIL) in Finland and addresses the issue of how to support the pupils with special needs in it. Specifically, this combination of a qualitative case study and quantitative survey examines (1) primary teachers' perceptions of differentiation, (2) the differentiation methods the teachers use in CLIL education and (3) the challenges of differentiation they identify. The qualitative phase was conducted in a school which offers CLIL education also to pupils with special needs following the principles of inclusive education. The results revealed that the teachers (n = 51) perceived differentiation in somewhat different ways. In general, the teachers differentiated their CLIL education in a fairly versatile manner with various teaching arrangements and methods and focused on the differentiation of the language. In addition, the teachers' perceptions of differentiation correlated with the differentiation practices they used. The greatest challenges of differentiation involved time, material and physical classroom environment. The study indicates that teachers should be more conscious of the nature of differentiation for it to be more purposeful and systematic. Schools should critically re-examine their structures and for instance co-teaching, class-size reduction or remedial teaching could be used more effectively.