Over the last decades major declines in urban house sparrow populations have been observed in north-western European cities, whereas suburban and rural house sparrow populations have remained rather stable or are recovering from previous declines. Pathogens that have the potential to cause large die-offs in passerines, such as Salmonella enterica subspecies enterica serotype Typhimurium and Yersinia pseudotuberculosis, have been suggested as jointly responsible for these declines. However, not much is known about the actual effect of urbanization on the prevalence of these bacteria in wild birds. From September 2013 until March 2014, 389 faecal samples were collected from apparently healthy house sparrows captured in 9 urban, 9 suburban and 18 rural populations across Flanders, Belgium. All of which were investigated for the presence of Salmonella Typhimurium and 342 were examined for the presence of Y. pseudotuberculosis. During the same period, full necropsy was performed on deceased house sparrows, received from Bird Rescue Centers, to determine the cause of death. Salmonella spp. were not isolated from the samples obtained during fieldwork, but 57% of the faecal samples carried Yersinia spp.. Four percent of these Yersinia spp. belonged to the pathogenic species Y. pseudotuberculosis. A pigeon specific Salmonella Typhimurium var. Copenhagen phage type DT99 and a Salmonella Typhimurium var. Copenhagen DT195 were isolated from granulomatous lesions present in the brains of two deceased house sparrows. These results suggest that Salmonella prevalence in Flemish house sparrows is very low, but if infections occur, these may result in death. On the contrary, Y. pseudotuberculosis is widely present in healthy house sparrows. The low prevalence of these infections renders a link with ongoing population declines in the urban regions of Belgium unlikely.