An understanding of the concepts of atoms and molecules is fundamental to the learning of chemistry. Any misconceptions and alternative conceptions related to these concepts which students harbor will impede much further learning. This paper identifies misconceptions related to the fundamental characteristics of atoms and molecules which Grade 12 students hold. Data were obtained by administration of semi-structured individual 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 relating to structure, composition, size, shape, weight, bonding and energy of molecules and structure, shape, size, weight and animistic perceptions of atoms. Many of the misconceptions identified parallel historical ideas of science. (Author)