ANATOM contains anatomical knowledge, using three different representation formalisms. The first is propositional representation (frames, constraints, logic), the second is a two-dimensional depictional representation (cell matrix), and the third is a three-dimensional model. Each has its own module for knowledge acquisition. The analysis of anatomical knowledge leads to meta-knowledge about the structure of anatomical knowledge. This is used to construct the knowledge acquisition tool Anatomy Description Language (ADL). Special attention is paid to the representation of the variations of the vessel system. This paper discusses the analysis of the anatomical knowledge and the propositional knowledge base and introduces briefly the concepts of depictional representation of neural fiber connections (without discussing depictional representation in general) and describes some problems of spatial inferences on three-dimensional anatomical structure.