In order to develop successful teaching approaches of transformations of matter, we need to know more about how young students develop understanding of these processes. In this longitudinal study I follow, mainly through interviews, 20 children from 7 to 11 years of age. I have chosen to examine the development of ideas about matter transformation of three different phenomena; one biological, one chemical and one physical. An early introduction of the concept of molecule is also made. Depending of the phenomenon some children in different ways use the molecule as a tool for understanding, while others do not. The children develop understanding of the different phenomena quite differently. They rely directly on their experiences when explaining the phenomena and the development of words and language seems extremely important. To understand the challenges that children meet trying to understand scientific explanations it is important to know about the complexity and individual variety of learning. A longitudinal study like this with a qualitative analysis has got the chance to catch this complexity and variation.