Guided instruction is an approach that fully explains the concepts and procedures that students are required to learn. It seems intuitive that this approach should increase student learning; however, there is evidence in the literature that this may not always be the case. We wanted to assess the effectiveness of our own repeated guided-instruction approach. This idea was tested in an introductory biology course on the topic of science-process skills and in a molecular biology course on DNA replication. Each course evaluated five concepts on their topic using five multiple-choice questions at four time points. Guided instruction for these topics was provided in the form of explicit lectures, discussions, questioning, case studies and multiple assessments. In both courses, mean test scores increased significantly over the four-test sequence, although not with each assessment or each concept. Increases in molecular biology were greater than in introductory biology. Content background and concept difficulty are two possible major factors contributing to this variation. In introductory biology, students struggled most with the concepts of definition of hypothesis and type I error. Further learning gains may be realised by providing and assessing context and content background to help students overcome difficult concepts. (Contains 3 figures.)