Students start the undergraduate quantum chemistry course with incomplete knowledge and many conceptual difficulties about quantum-chemical concepts. This work investigated the impact an undergraduate quantum chemistry course has on students’ knowledge and understanding of atomic orbitals, molecular orbitals and related concepts. A “post-factum” analysis of examination data from this course reveals that students; do not have a clear understanding of the concepts of atomic and molecular orbitals as well as of Slater determinants; have difficulty in understanding the conceptual similarity between real and complex mathematical forms of atomic orbitals; confuse the various atomic orbital representations; and, do not realise the approximate nature of atomic orbitals for many-electron atoms. Difficulties with other related concepts are revealed also. Some promising strategies for instruction and suggestions for secondary and general chemistry curricula are discussed.