Interest in ubiquitous low-cost unmanned aerial vehicles (UAVs) for use in aeromagnetic surveying has grown dramatically over the past decade. While their appeal is alluring, caution is called for as high-quality airborne magnetometry requires diligent system design and performance qualification. This paper discusses considerations and trade-offs in UAV-based magnetometry, standard measures to qualify performance, and application to magnetic anomaly detection (MAD). The apparent simplicity of towed-bird installations needs careful consideration. Logistical complexities, stability, and safety issues aside, critical compensation for time-varying swing effects is seldom, if at all, standard practice. While well-compensated fixed-mount sensor installations are preferable, they require careful attention to a number of unique aspects including the complex magnetic signatures of typical UAVs. The paper introduces a novel anomaly detection method that is based on the entropy of the total-field magnetometer signal, gated by an analogous measure obtained from a vector magnetometer. Two field studies using a fixed-mount single-magnetometer configuration on a helicopter UAV empirically demonstrate the application of the performance measures and the performance of the MAD method. Notably, the latter clearly illustrates the importance of sound aeromagnetic compensation and enhances the output of an earlier entropy-based detection method.