The author argues that the well-formulated problem list is essential for both organizing and evaluating diagnostic thinking. He considers evidence of deficiencies in problem lists in the medical record. He observes a trend among medical trainees toward organizing notes in the medical record according to lists of organ systems or medical subspecialties and hypothesizes that system-based documentation may undermine the art of problem formulation and diagnostic synthesis. Citing research linking more sophisticated problem representation with diagnostic success, he suggests that documentation style and clinical reasoning are closely connected and that organ-based documentation may predispose trainees to several varieties of cognitive diagnostic error and deficient synthesis. These include framing error, premature or absent closure, failure to integrate related findings, and failure to recognize the level of diagnostic resolution attained for a given problem. He acknowledges the pitfalls of higher-order diagnostic resolution, including the application of labels unsupported by firm evidence, while maintaining that diagnostic resolution as far as evidence permits is essential to both rational care of patients and rigorous education of learners. He proposes further research, including comparison of diagnostic efficiency between organ- and problem-oriented thinkers. He hypothesizes that the subspecialty-based structure of academic medical services helps perpetuate organ-system-based thinking, and calls on clinical educators to renew their emphasis on the formulation and documentation of complete and precise problem lists and progressively refined diagnoses by trainees.