The purpose of this research conducted in Burkina Faso was to assess i) the quality and reliability of the recording of immunization data and ii) the impact of 13-valent pneumococcal conjugate vaccine (PCV13) on carriage and disease due to the pneumococcus, during the first five years of routine use in infants. Data were obtained through a series of cross-sectional surveys and a retrospective patient chart review, complemented by a literature review. We identified a range of issues around the recording of individual vaccination data, including the lack of standardization of recording forms, and inconsistent data recording practices. Data on pneumococcal carriage and disease indicate evidence of direct effects of PCV13 among vaccinated cohorts, but no evidence of herd immunity among unvaccinated persons. These findings can inform corrective health policy decision-making, including the adoption of an alternative vaccine strategy favoring the direct vaccination of older children and adults to optimize impact.