Due to a Europe-wide decline of grey partridge (Perdix perdix) and pheasant (Phasianus colchicus) populations, this study was conducted focusing on the county of Bavaria, south Germany. The aim was to assess the health status of game birds and identify possible causes of decline. For this purpose 203 pheasants and 11 partridges were examined during the 2011 hunting season. Pathologic examinations were conducted including examinations for parasites and bacteria. Due to public health significance, a screening for Salmonella sp., as well as real-time polymerase chain reaction examinations for Campylobacter sp. and Mycobacterium avium ssp. avium, were done. Because pesticides and land-usage can possibly influence bird numbers, the birds were screened for environmental toxin residues, including neonicotinoid insecticides, and land-usage data were correlated with the hunting bags. The result was a very-strong positive correlation of set-aside areas and a less-strong negative correlation of maize cultivation acreage. More than 90% of the birds had a good health status; only individuals showed pathologic alterations. For example, avian tuberculosis was found in two pheasants and a severe capillariosis in two partridges. A possible role of female reproductive disorders has to be confirmed in further investigations. In conclusion, results suggest the decrease of set-aside areas could be a possible reason for decline.