E-learning strategies for the teaching unit Structure and States of Matter were developed. Students’ achievements and the percentages of misconceptions were compared between experimental groups taught using web-based learning material (WBLM) used as homework after conventional teaching at school (EG1), and at school settings (EG2) with the control group (CG) taught with the teacher-centred approach. The results indicated that WBLM has potential in teaching since EG1 and EG2 students had higher achievements than CG students did on tests of knowledge. Appropriate statistical procedures were used to control the effects of students’ verbal and non-verbal intelligence, as well as their prior knowledge regarding the Particulate Nature of Matter. Certain misconceptions were also revealed in all groups of students, mostly related to transferring macroscopic properties to submicroscopic particles.