This article discusses lessons learned from clinical trials with pneumococcal conjugate vaccines (PCVs). A review of major clinical trials investigating PCV efficacy, this article provides the context to explore challenges associated with studying pneumococcal pneumonia and vaccine efficacy, particularly related to non-bacteremic disease, serotypes, and radiograph interpretation. Throughout these clinical trials, improving the pneumonia diagnosis specificity increased vaccine efficacy estimates. Additional analysis suggests this improvement may come at a cost of detecting much less of the disease burden. The article concludes with a discussion of the potential value of C-reactive protein as an adjunctive marker in measuring PCV efficacy against non-bacteremic pneumococcal pneumonia.