The objective of this study was to examine middle school students' developing understanding of the nature of matter and to compare middle school students' ideas to those of elementary schools students, as was done by Nakhleh and Samarapungavan ["J Res Sci Teach" 36(7):777-805, 1999]. Nine middle school students were interviewed using a scripted, semistructured interview. The interview probed students' understanding of the composition and particulate (atomic/molecular) structure of a variety of material substances; the relationship between particulate structure and macroscopic properties such as fluidity and malleability; as well as understanding of processes such as phase transition and dissolving. The results indicate that most of the middle school students interviewed knew that matter was composed of atoms and molecules and some of them were able to use this knowledge to explain some processes such as phase transitions of water. In contrast, almost no elementary students knew that matter was composed of atoms and molecules. However, the middle school students were unable to consistently explain material properties or processes based on their knowledge of material composition. In contrast to elementary school students, who had scientifically inaccurate but relatively consistent (macrocontinuous or macroparticulate) knowledge frameworks, the middle school students could not be classified as having consistent knowledge frameworks because their ideas were very fragmented. The fragmentation of middle school students' ideas about matter probably reflects the difficulty of assimilating the microscopic level scientific knowledge acquired through formal instruction into students' initial macroscopic knowledge frameworks.