This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students' understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student's alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified by cognitive levels and then randomly assigned to experimental (PBL, 40 students) and control (lecture-style teaching, 38 students) groups. Following a preparatory lesson where activation and remediation of existing knowledge occur, a pre-test was given, and no significant difference was found between the two groups of students (p > .05). After the instruction was completed, a post-test and also a questionnaire related to the quality of the problem, the teacher's role and group functioning were administered. Results from the post-test of both groups (p < .05) and questionnaire showed that PBL is affective on students' achievement, remedying formation of alternate conceptions and also social skills.