In the wake of increasing evidence that students' positive attitudes towards science particularly in chemistry and physics change strikingly as they move up in school, this study explores student perception of intrinsic and extrinsic factors that make them feel cognitive load in learning physics, chemistry and biology resulting in difficulty to learn these subjects. A four-fold classification of student perception of factors related to nature of subjects and their teaching learning with varying level of control over them for teachers is designed to develop a questionnaire, which was used to obtain student rating on difficulties. The sample is 300 high school students from Kerala. The differences among student difficulty in science disciplines is more due to the nature of subject matter and is minimal from factors related to teaching-learning over which teachers have a high degree of control. Results indicate that intrinsic cognitive load inherent in the nature of physics and to a fair extent in chemistry interacts with extrinsic factors in teaching and especially in students' effort to learn them to make these subjects more difficult to learn. A good proportion of variation in student perception of difficulties in physics, chemistry and biology originates from what students feel generally about the nature of content included in school science and the way it is taught which calls for school science curriculum reforms.