Primary school students often do not have differentiated conceptions of human organs and organ systems. As understanding the inner structure of the human body is an elementary prerequisite for the development of health awareness, appropriate forms of teaching must be developed to modify students' fragmented preconceptions about the inside of their bodies into scientifically accurate concepts. Anatomical models are considered a medium to raise awareness of organs and their systemic integration; however, only a few studies have investigated their effectiveness in the context of primary school. This intervention study, therefore, examines the effect of anatomical models on the conceptions of inner organs in German primary school students (N = 45) in a pretest, posttest, and follow-up test design with anatomy teaching between pre- and posttests. Concepts were measured using students' drawings in two treatment groups (anatomical models versus anatomical illustrations). While in both treatment groups students' conceptions changed toward more scientific concepts, there was little difference in the changes between the two groups. There were even indications that the students of the control group showed more pronounced increases, for example, in long-term systemic integration of the organs. We discuss the reasons for this and furnish recommendations for effective teaching practices.