In search for the nature of understanding of basic science in a clinical context, eight medical students were interviewed, with a focus on their view of the discipline of anatomy, in their fourth year of study. Interviews were semi-structured and took place just after the students had finished their surgery rotations. Phenomenographic analysis was used to explore how the students took on learning the subject matter. An understanding of anatomy comprising purely anatomical knowledge was found hard to discern in the interviews. The ways of understanding anatomy evolved into four categories: contextualisation, visualisation, selection and anatomical language. The informants developed two qualitatively different forms of understanding, conceptual and perceptual, when approaching the subject from a clinical point of view. Aspects of understanding in relation to the nature of anatomical knowledge are discussed.