Proceedings of the 4th International Conference on Theory and Application of Diagrams, Stanford, CA, USA in June 2006. 13 revised full papers, 9 revised short papers, and 12 extended abstracts are presented together with 2 keynote papers and 2 tutorial papers. The papers are organized in topical sections on diagram comprehension by humans and machines, notations: history, design and formalization, diagrams and education, reasoning with diagrams by humans and machines, and psychological issues in comprehension, production and communication.