Concerns about public health risks of intensive animal production in The Netherlands continue to rise, in particular related to outbreaks of infectious diseases. The aim was to investigate associations between the presence of farm animals around the home address and Q fever and pneumonia.Electronic medical record data for the year 2009 of all patients of 27 general practitioners (GPs) in a region with a high density of animal farms were used. Density of farm animals around the home address was calculated using a Geographic Information System. During the study period, a large Q fever outbreak occurred in this region. Associations between farm exposure variables and pneumonia or 'other infectious disease', the diagnosis code used by GPs for registration of Q fever, were analyzed in 22,406 children (0-17 y) and 70,142 adults (18-70 y), and adjusted for age and sex. In adults, clear exposure-response relationships between the number of goats within 5 km of the home address and pneumonia and 'other infectious disease' were observed. The association with 'other infectious disease' was particularly strong, with an OR [95%CI] of 12.03 [8.79-16.46] for the fourth quartile (>17,190 goats) compared with the first quartile (<2,251 goats). The presence of poultry within 1 km was associated with an increased incidence of pneumonia among adults (OR [95%CI] 1.25 [1.06-1.47]).A high density of goats in a densely populated region was associated with human Q fever. The use of GP records combined with individual exposure estimates using a Geographic Information System is a powerful approach to assess environmental health risks.