Since its inception in 1869, the periodic system — icon of modern chemistry — has suffered from the problematic accommodation of the rare-earth elements. The substance of this paper intends to retrace Mendeleev’s shifting attitudes with regard to the rare-earth crisis during the period 1869–1871. Based on a detailed examination of Mendeleev's research papers from that period, it will be argued that the rare-earth crisis played a key role in inducing a number of important changes in Mendeleev’s philosophical viewpoints with regard to the epistemological concept of a chemical element and the nature of elementary groups. Many of Mendeleev's most cherished beliefs got endangered by the nature of these elements. Their mystifying properties forced him to revise his ideas about primary and secondary groups, the elements as basic and simple substances, and the use of short and long form tables. They made him question the validity and universality of the periodic law, and led him into hypothesizing about the internal structure of matter and constitution of atoms.
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