Pneumococcal conjugate vaccines have had unprecedented success in controlling vaccine-type invasive pneumococcal disease. As serotype replacement and the complexity of designing vaccines to multiple capsular polysaccharides ultimately pose a threat to these vaccines, the development of alternative protein vaccines is important. Protein vaccines offer the promise of extended serotype coverage, reduced cost, and improved protection against otitis media and pneumococcal pneumonia. As placebo-controlled trials are not currently ethically justifiable, human pneumococcal challenge models using prevention of carriage as a test endpoint offer an attractive link between preclinical studies and clinical efficacy trials. Experimental human pneumococcal carriage studies offer a means of describing mechanisms of protection against carriage and a clinical tool to choose between vaccine candidates.