Background Early childhood caries (ECC) describes dental caries affecting children aged 0–71 months. Current research suggests ECC has important aetiological bases during the first year of life. Gaps in knowledge about disease progression prevent the effective and early identification of ‘at risk’ children. Aim To conduct a systematic review of research studies focusing on (a) acquisition and colonization of oral bacteria and ECC and (b) risk and/or protective factors in infants aged 0–12 months. Design Ovid Medline and Embase databases (1996–2011) were searched for RCT, longitudinal, cross‐sectional and qualitative studies. Two investigators undertook a quality assessment for risk of bias. Results Inclusion criteria were met for (a) by four papers and for (b) by 13 papers; five papers were rated medium or high quality. Bacterial acquisition/colonization and modifying factor interrelationships were identified, but their role in the caries process was not clarified. Key risk indicators were infant feeding practices (nine papers), maternal circumstances and oral health (6) and infant‐related oral health behaviours (4). Conclusion This review confirmed that factors occurring during the first year of life affect ECC experience. Despite heterogeneity, findings indicated maternal factors influence bacterial acquisition, whereas colonization was mediated by oral health behaviours and practices and feeding habits.