Little is known about the intestinal microflora of Common Terns (Sterna hirundo) and their capacity to disseminate human gastrointestinal pathogens along migratory flyways. Common Tern chicks on Pettit Island in Barnegat Bay, New Jersey, USA, were evaluated for carriage of bacterial and protozoan pathogens. Oropharyngeal and cloacal swabs were taken for culture-based detection of bacterial gastrointestinal pathogens during the 2009 and 2010 breeding seasons. Bulk fecal samples were also taken during the 2010 nesting season to determine Cryptosporidium oocyst loads. Of 125 birds sampled in 2009, none carried Salmonella and only one carried Campylobacter. Moreover, the majority of birds sampled in the 2009 breeding season carried Escherichia coli and Klebsiella ozaenae, members of bacterial family Enterobacteriaceae. In 2010, one of the 54 birds sampled carried Salmonella and none had Campylobacter in their intestines. Similar to the birds sampled in 2009, the 2010 cohort showed relatively high carriage of E. coli and K. ozaenae. Microscopic examination of fecal smears obtained in 2010 revealed that 39 of 54 Common Tern chicks had microscopic structures consistent with Cryptosporidium oocysts in their intestines. These data indicate that Common Tern chicks in Barnegat Bay present low to no threat to public health through the spread of human gastrointestinal pathogens.