Since the basic concepts in science education form the base of more advanced science topics, they should be taught correctly and meaningfully in primary and secondary school for the sake of an effective science education. This study is conducted to detect 6(th) and 7(th) grade students' misconceptions on "photosynthesis" and "respiration" units and to determine the effect of the developed computer assisted instruction (CAI) material on removal of these misconceptions. The misconceptions were determined by clinical interviews conducted with the help of the prepared question cards. In order to remove the misconceptions, animations were developed to animate each picture in the question cards. The students were made to interact with these animations and misconceptions were tried to be removed by this way. (C) 2010 Elsevier Ltd. All rights reserved.