We report from a longitudinal study of young children’s understanding of matter and its transformations. Interviews have been carried out regularly concerning their conceptions of three different natural phenomena. These conceptions have a personal framing of experiences or idioms that becomes apparent as a result of the longitudinal design. We have also made an early (at the age of 6-7 years) introduction of the concept of molecule. Depending on the phenomenon some of he children in different ways use the molecule as a tool for understanding, while others do not. By focusing on a few examples which we will analyse in detail, we will argue that longitudinal studies can give important information about children’s learning that other kinds of studies do not.