The Periodic Table of Elements (PTE) is one of the organizing principles in chemistry. Originally it was a list of elements (as substances). Later, the PTE developed into a list of atoms of the elements. However, isotopes and allotropes are difficult to integrate into the PTE. Therefore, difficulties in understanding these terms can be expected. The investigation set off to study secondary school students' concepts of isotopes and allotropes and how the concepts are linked to the PTE. Three specific research questions were addressed: (a) How do secondary school students describe the relationship between fundamental particles constituting an atom? (b) How do they conceive isotopes? and (c) What are students' concepts of graphite and diamond? Multiple choice items were given to 3074 senior high school students. In addition, six interviews were conducted with senior high school students. The data analysis revealed students' alternative concepts, which distinguished between standard atoms and atoms of isotopes. Standard atoms contain neutrons and protons in equal numbers and are more stable. The atomic masses are expressed as integers. Moreover, students considered graphite and diamond as isotopes. The analysis of the results shows that students actively tried to make sense of what they had experienced. © 2003 Wiley Periodicals, Inc. J Res Sci Teach 40: 257–277, 2003