The emergence and persistence of antimicrobial resistance, which are driven by multiple factors including indiscriminate use of antibiotics, impede the control of infectious diseases. Despite the high disease burden in sub-Saharan Africa and the resultant health and economic consequences, limited data exist to quantify the contribution of different factors to the current prevalence of antimicrobial resistance. We used the PRISMA 2009 guidelines to conduct a systematic review of studies on antibiotic-resistant enteric bacteria in Eastern Africa to identify these factors and their contribution to the emergence, amplification, persistence and dissemination of antimicrobial resistance in humans and animals. We searched PubMed and Google Scholar databases and identified 2,155 probable articles from Kenya, Tanzania, Uganda, Ethiopia, Rwanda and Burundi, published between 1974 and 2013. After full-text review, 89 studies on humans and 28 on animals that report resistance in Salmonella, Shigella, Escherichia coli and Vibrio sp. satisfied the inclusion criteria. Unlike animal studies, most (98%) human studies were based on hospital- (rather than community-wide) sampling. Although high levels of antimicrobial resistance were reported, variations in documented methodologies and results precluded any conclusions about the magnitude and trends of antimicrobial resistance. To remedy this, we propose minimum reporting guidelines for the level of detail that should be explicitly provided for study designs, sample testing and data reporting; details that are requisite for future meta-analyses. This approach, coupled with establishment of a robust regional surveillance network should, over time, build the pool of data required for evidence-based interventions aimed at controlling antimicrobial resistance.