This work investigates the formation of particular student profiles based on of their ideas relating to basic characteristics of the atom. Participants were secondary students of 8th, 10th and 12th grades from Northern Greece (n = 421), with specific cohort characteristics e.g. age, grade and class curriculum, and individual differences, e.g. formal reasoning, field dependence-independence and divergent thinking. Analysis of data from four tasks concerning the characteristics of the atom, linked to identity and behaviour, revealed a significant number of students' misconceptions. A joint dimension reduction and clustering method was applied to outcomes from these four tasks and a four-cluster solution emerged as the most conceptually meaningful. An inspection of the relevant student profiles indicated that three tasks were the most important in the formation of the clusters; one task concerning the understanding of the differences between the atom and other particles of the microcosm and two tasks concerning relations between relevant micro- and macro- characteristics. Furthermore, individual differences could effectively discriminate between student profiles. Generally, students' performance in the above tasks was positively associated to their performance in the three cognitive factors, whereas formal reasoning contributed the most to this discrimination. Although the distribution of student cohort characteristics across student profiles was not clearly different, it seemed that the curriculum also played a noticeable role in the formation of profiles. Relevant implications for the educational practice were also discussed.