This paper discusses some problems in the philosophy of classification based on a discussion of the periodic system of chemistry and physics. The emerging interdisciplinary field ‘philosophy of classification’ is briefly introduced and related to the field of knowledge organization (KO) within Library and Information Science (LIS). It is argued that KO needs to be better integrated with the broader field of classification theory and research. The paper considers some core issues such as whether classifications are pragmatic human tools or neutral reflections of nature, how classifications are related to subject theories (theories of what is being classified), and issues related to different ideals in scientific methodology, including empiricism, rationalism, historicism and pragmatism. It is argued that empiricism and rationalism (alone or in combination) are not sufficient to explain scientific progress, including the development of the periodic table. The existence of alternatives to the periodic system is also considered.