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Objectives: Determine if clinical decision support (CDS) malfunctions occur in a commercial electronic health record (EHR) system, characterize their pathways and describe methods of detection., Methods: We retrospectively examined the firing rate for 226 alert type CDS rules for detection of anomalies using both expert visualization and statistical process control (SPC) methods over a five year period. Candidate anomalies were investigated and validated., Results: Twenty-one candidate CDS anomalies were identified from 8,300 alert-months. Of these candidate anomalies, four were confirmed as CDS malfunctions, eight as false-positives, and nine could not be classified. The four CDS malfunctions were a result of errors in knowledge management: 1) inadvertent addition and removal of a medication code to the electronic formulary list; 2) a seasonal alert which was not activated; 3) a change in the base data structures; and 4) direct editing of an alert related to its medications. 154 CDS rules (68%) were amenable to SPC methods and the test characteristics were calculated as a sensitivity of 95%, positive predictive value of 29% and F-measure 0.44., Discussion: CDS malfunctions were found to occur in our EHR. All of the pathways for these malfunctions can be described as knowledge management errors. Expert visualization is a robust method of detection, but is resource intensive. SPC-based methods, when applicable, perform reasonably well retrospectively., Conclusion: CDS anomalies were found to occur in a commercial EHR and visual detection along with SPC analysis represents promising methods of malfunction detection.