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Recognizing anatomical structure properties depicted within digital representations may be the first step to conceptual understanding. Comparing stereoscopic and non-stereoscopic visualizations, there is little evidence whether stereoscopic visualisations better support the recognition of anatomical structure properties. Likewise, insufficient indication is given whether working with stereoscopic visualizations is in connection with situational variables such as increased situational intrinsic motivation and decreased visual attention performance. To clarify these queries, the present study focused on two e-learning environments dealing with the anatomy and physiology of the nasal cavity and with the anatomy and physiology of hearing. Participants were 8th grade students and teacher students. Working with stereoscopic imagery instead of non-stereoscopic imagery, both succeeded better in absolving anatomical structure-related tasks such as estimating anatomical spatial-relationships. Working with stereoscopic visualizations neither led to increased situational intrinsic motivation nor to decreased visual attention performance. On the one hand, the results show that stereoscopic visualization technology can be used without having any novelty effects. On the other hand, stereoscopic visualizations can be used without having impairments on visual working memory. Coming from these findings it should be investigated, whether the enhanced performance on anatomical structure-related tasks due to stereoscopic imagery can be used to also enhance conceptual understanding.