The development of a comprehensive microbiological testing strategy has been a core principle in the conception and design of the Pneumonia Etiology Research for Child Health (PERCH) project [1] . In formulating the most effective approach for respiratory diagnosis, we determined that a multiplex molecular diagnostic platform would be an essential component in our approach. Many of the technical and operational considerations encountered through this process proved relevant to the overall design of the project. We describe here the theoretical and practical challenges encountered in the evaluation and selection of a molecular platform for the diagnosis of pneumonia.