The purpose of this study was twofold: (1) to understand the conceptual frameworks that sixth-grade students use to explain the nature and structure of matter and molecules; and (2) to assess the effectiveness of two alternate instructional units in helping students change those conceptions. The study involved 15 sixth-grade classes taught by 12 teachers in each of 2 successive years. Student misconceptions were investigated during the first year. Clinical interviews administered to 24 students and tests administered to 365 students revealed that their thinking about the nature of matter and about physical changes in matter differed from canonical scientific thinking in a number of ways. The main purpose of the second year of the study was to compare the effectiveness of the original commercial teaching unit with revised curriculum materials in promoting student understanding of matter and molecules. Posttest scores for both years were compared. The differences in posttest scores concerning aspects of matter and molecules were statistically significant for 9 of the 10 conceptual categories studied. Implications for science teaching and curriculum development are discussed. Conceptual frameworks, charts of student conceptions and tasks, a copy of the pre/posttest, and the interview protocol and analysis system are appended. (CW/Author)