BACKGROUND: Cambodia introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in January 2015 using a 3+0 dosing schedule and no catch-up campaign. We investigated the effects of this introduction on pneumococcal colonisation and invasive disease in children aged <5 years. METHODS: Six colonisation surveys were done between January 2014 and January 2018 in children attending the outpatient department of a non-governmental paediatric hospital in Siem Reap. Nasopharyngeal swabs were analysed by phenotypic and genotypic methods to detect pneumococcal serotypes and antimicrobial resistance. Invasive pneumococcal disease (IPD) data for January 2012 - December 2018 were retrieved from hospital databases. Pre-PCV IPD data and pre-/post-PCV colonisation data were modelled to estimate vaccine effectiveness (VE). RESULTS: Comparing 2014 with 2016-2018, and using adjusted prevalence ratios, vaccine effectiveness (VE) estimates for colonisation were 16.6% (95% CI 10.6-21.8) for all pneumococci and 39.2% (26.7-46.1) for vaccine serotype (VT) pneumococci. There was a 26.0% (17.7-33.0) decrease in multi-drug resistant pneumococcal colonisation. IPD incidence was estimated to have declined by 26.4% (14.4-35.8) by 2018, with a decrease of 36.3% (23.8-46.9) for VT IPD and an increase of 101.4% (62.0-145.4) for non-vaccine serotype IPD. CONCLUSIONS: Following PCV13 introduction into the Cambodian immunisation schedule there have been declines in VT pneumococcal colonisation and disease in children aged <5 years. Modelling of dominant serotype colonisation data produced plausible vaccine effectiveness estimates.