In 2002, the National Legionella Outbreak Detection Program was implemented in the Netherlands to detect and eliminate potential sources of organisms that cause Legionnaires’ disease (LD). During 2002–2012, a total of 1,991 patients with LD were reported, and 1,484 source investigations were performed. Of those sources investigated, 24.7% were positive for Legionella spp. For 266 patients with LD, 105 cluster locations were identified. A genotype match was made between a strain detected in 41 patients and a strain from a source location. Despite the systematic approach used by the program, most sources of LD infections during 2002–2012 remained undiscovered. Explorative studies are needed to identify yet undiscovered reservoirs and transmission routes for Legionella bacteria, and improved laboratory techniques are needed to detect Legionella spp. in samples with a high background of microbial flora (such as soil).