Many graduates of various levels and disciplines appear unable to practically apply their knowledge in problem solving situations. However, few education systems are adopting modern education practices such as visualization skills that intrinsically motivate and engage learners and are at the same time flexible enough to consider students' aspirations and interests. Such systems make learning more relevant, meaningful and enjoyable to the learners and improve exit performances. In such a system, the role of the teacher is that of a facilitator and not instructor. The purpose of this study was to identify three-dimensional (3D) visualizations that could aid comprehension and perception of cytoplasmic structure, geo-referenced graphical data and understanding of spatial relationships in Biology. A qualitative research approach was used to ascertain from university lecturers (n = 13) what convictions, beliefs and experiences they have had with their students that related to the use of visualization skills. Skills most required included interpretation of 2 and 3D structures as well as their rotation in space. A survey was also carried out among cell biology first year students (n = 145) and second year students (n = 45) of the School of Life and Environmental Studies at the University of Natal in order to precisely determine aspects of three-dimensionality and visual skills suspected to cause conceptual difficulties. Quantitative data analysis (the non parametric Mann-Whitney U-Wilcoxon Test at a confidence level of 0.05) showed that the most deficient skills in the learners included pattern folding (projecting 2D material into 3D objects), orientation of form (identifying 3D objects that are oriented differently) and rotation (identifying 3D objects from top and front views). These findings corroborate qualitative analysis of lecturers' opinions and convictions. An educational computer game is proposed with the aim of ameliorating these problems. It is recommended that visualization skills should be incorporated into the Biology curriculum for all undergraduate students within the first year of the course. (Contains 4 figures.)