Clinical documents frequently contain a list of a patient's medications. Missing information about the dosage, route, or frequency of a medication impairs clinical communication and may harm patients. We examined 253 medication lists. There were 181 lists (72%) with at least one medication missing a dose, route, or frequency. Missing information was judged to be potentially harmful in 47 of the lists (19% of 253) by three physician reviewers (kappa=0.69). We also observed that many lists contained additional information included as annotations, prompting a secondary thematic analysis of the annotations. Fifty-five of the 253 lists (22%) contained one or more annotations. The most frequent types of annotations were comments about the patient's medical history, the clinician's treatment plan changes, and the patient's adherence to a medication. Future development of electronic medication reconciliation tools to improve medication list completeness should also support annotating the medication list in a flexible manner.