Abstract Background There is growing interest in health risks of residents living near concentrated animal feeding operations (CAFOs). Previous research mostly focused on swine CAFOs and self-reported respiratory conditions. The aim was to study the association between the presence of swine, poultry, cattle and goat CAFOs and health of Dutch neighbouring residents using electronic medical records from general practitioners (GPs). Methods Data for the year 2009 were collected of 119,036 inhabitants of a rural region with a high density of CAFOs using information from GIAB (high exposed population). A comparison was made with GP data from 78,060 inhabitants of rural areas with low densities of CAFOs (low exposed population). Associations between the number of CAFOs near residents’ homes and morbidity were determined by multilevel (cross-classified) logistic regression. Results In 2009, the prevalence of most respiratory and gastrointestinal conditions was similar in the high and low exposed population. Exceptions were pneumonia, atopic eczema and unspecified infectious diseases with an increased prevalence, and sinusitis with a decreased prevalence in the high exposed population. Within the high CAFO density region, the number of poultry, cattle and swine CAFOs near residents’ homes was not associated with allergic, respiratory or gastrointestinal conditions. Conversely, each additional goat CAFO within the postal code area of residents’ homes significantly increased the odds of unspecified infectious disease and pneumonia by 87 and 41 percent, respectively. Conclusions Using GP records, pneumonia and unspecified infectious diseases were positively associated with the number of goat CAFOs near residents’ homes, but no association was found between swine, cattle, and poultry CAFOs and respiratory, allergic or gastrointestinal conditions.