An understanding of the concepts of atom and molecule is fundamental to the learning of chemistry. Any misconceptions and alternative conceptions that students harbor about these concepts will impede further learning. This article identifies misconceptions related to the fundamental characteristics of atoms and molecules which Grade-12 students hold. Data were obtained by administration of semistructured interviews to a stratified, random sample of 30 students of differing abilities and backgrounds in science. Fifty-two misconceptions were observed and are reported. These are grouped into 11 categories. Six relate to the structure, composition, size, shape, weight, bonding, and energy of molecules; five relate to the structure, shape, size, weight, and animistic perceptions of atoms. Some of the misconceptions identified parallel the historical development of scientific concepts.