Abstract Background Vaccines are highly effective at preventing infectious diseases in children, and prevention is especially important in resource-limited countries where treatment is difficult to access. In Honduras, the World Health Organization (WHO) reports very high immunization rates in children. To determine whether or not these estimates accurately depict the immunization coverage in non-urban regions of the country, we compared the WHO data to immunization rates obtained from a local database tool and community health center records in rural Intibucá, Honduras. Methods We used data from two sources to comprehensively evaluate immunization rates in the area: 1) census data from a local database and 2) immunization data collected at health centers. We compared these rates using logistic regression, and we compared them to publicly available WHO-reported estimates using confidence interval inclusion. Results We found that mean immunization rates for each vaccine were high (range 84.4 to 98.8 percent), but rates recorded at the health centers were significantly higher than those reported from the census data (p≤0.001). Combining the results from both databases, the mean rates of four out of five vaccines were less than WHO-reported rates (p p=0.03). The rates by individual vaccine were similar across townships (p >0.05), except for diphtheria/tetanus/pertussis vaccine (p=0.02) and oral polio vaccine (p Conclusions Immunization rates in Honduras were high across data sources, though most of the rates recorded in rural Honduras were less than WHO-reported rates. Despite geographical difficulties and barriers to access, the local database and Honduran community health workers have developed a thorough system for ensuring that children receive their immunizations on time. The successful integration of community health workers and a database within the Honduran decentralized health system may serve as a model for other immunization programs in resource-limited countries where health care is less accessible.