In this study it was aimed to i) diagnose the topics that are perceived as difficult at the level of 6-8 science classes and ii) find out the reasons behind of these difficulties as well as propose suggestions to remedy these difficulties. Eighteen science teachers and three hundred students attending different types of secondary schools participated in the study. In the study in which qualitative and quantitative methods were used 114 science topics were listed to diagnose the topics that are perceived as difficult. Participants were noted their ideas regarding the topics as "easy", "moderate" and "difficult." Topic difficulty index (TDI) was used to determine the level of difficulty. To find out the reasons behind the difficulties, five teachers and ten pupils who indicated the topics of the highest difficulties were interviewed. The results of the study showed that i) the topics that have the TDI value over %25 are mostly related to physical processes and they are followed the topics about living organisms and life, matter and change, The World and the Universe, respectively, ii) there is not an exact overlap between the topics that are perceived as difficult both by teachers and the students, iii) there are several reasons (e.g., the level of abstractness of the concepts, overloading of the content, mathematical skill, language etc.) behind the difficulties. The possible effects of these results on science education and their importance regarding learning, teaching, assessment as well as curriculum development are critically analyzed and some suggestions are made to remedy the difficulties. (Contains 1 figure and 4 tables.)