Bacterial pneumonia is a substantial cause of childhood morbidity and mortality worldwide, but determination of pathogen-specific burden remains a challenge. In less developed settings, the WHO recommended guidelines are useful for initiating care, but are non-specific. Blood culture has low sensitivity, while radiological findings are non-specific and do not discriminate between viral and bacterial causes of pneumonia. In vaccine probe studies, efficacy is dependent on the specificity of the study outcome to detect pneumonia and the impact of the vaccine on the selected outcome, and may underestimate the true burden of bacterial pneumonia. The rising incidence of antibiotic resistance, emerging respiratory pathogens, potential replacement pneumococcal disease following widespread introduction of pneumococcal polysaccharide-protein conjugate vaccine, the limited specificity of chest radiography, and the poor sensitivity of blood culture are substantial obstacles to accurate surveillance. We provide an overview of the diagnostic challenges of bacterial pneumonia and highlight the need for refining the current diagnostic approach to ensure adequate epidemiological surveillance of childhood pneumonia and the success, or otherwise, of any immunisation strategies.