Medical devices based on embedded systems are ubiquitous in clinical settings. Increasingly, they connect to networks and run off-the-shelf operating systems vulnerable to malware. But strict validation requirements make it prohibitively difficult or costly to use anti-virus software or automated operating system updates on these systems. Our add-on monitoring system, WattsUpDoc, uses a traditionally undesirable side channel of power consumption to enable run-time malware detection. In our experiments, WattsUpDoc detected previously known malware with at least 94% accuracy and previously unknown malware with at least 85% accuracy on several embedded devices—detection rates similar to those of conventional malware-detection systems on PCs. WattsUpDoc detects malware without requiring hardware or software modifications or network communication.