The systems basis for medical errors is widely acknowledged. How to improve organizations to perform more effectively is less well understood. Complex systems concepts can be used to analyze the origins of medical errors as well as methods for changing the system to reduce their frequency or eliminate them. The key to this analysis is recognizing that the source of a particular error does not lie in a sequence of events that occurred in a particular circumstance, but rather in the set of possibilities that can occur and the ability of the organization to match the set of necessary possibilities with a corresponding set of appropriate actions. An analysis of the space of possibilities enables an identification of the “weak links” in organizational structures. Application to the problem of prescription fulfillment suggests that a likely source of the widespread errors in this context is the convergence of communication from diverse specialists to the pharmacists or administering nurse. Specific recommendations follow from this for organizational improvement either by increasing the redundancy of this communication channel, or by developing care teams that include medical professionals associated with local groups of patients. Effective and ineffective use of automation is discussed.