The concept of the atom is one of the building blocks of science education. Although the concept is a foundation for students' subsequent learning experiences, it is difficult for students to comprehend because of common misconceptions and its abstractness. The purpose of this study is to examine junior high school students' (ages 12-13) ideas about the shape and size of the atom and the evolution of these ideas over 2 years. The study's sample size was 126 students, including 76 sixth-grade and 50 seventh-grade students. The educational curriculum and relevant literature guided the development of a questionnaire that consisted of three open-ended questions intended to determine students' knowledge of the structure and physical properties of the atom. After administering the questionnaire, collected data were analysed qualitatively. The study shows that students had difficulty developing a mental image of the atom, and contrary to the conclusions of other studies, students demonstrated a preference for working with complex and abstract models.