Because of overpopulation, stray/feral cats were captured on military bases in Iraq as part of the US Army Zoonotic Disease Surveillance Program. Blood samples were collected from 207 cats, mainly in Baghdad but also in North and West Iraq, to determine the prevalence of Bartonella and Toxoplasma infections. Nine (4.3%) cats, all from Baghdad, were bacteremic with B. henselae type I. Seroprevalence was 30.4% for T. gondii, 15% for B. henselae, and 12.6% for B. clarridgeiae. Differences in Bartonella prevalence by location were statistically significant, because most of the seropositive cats were from Baghdad. There was no association between T. gondii seropositivity and either of the two Bartonella species surveyed. This report is the first report on the prevalence of Bartonella and T. gondii among stray cats in Iraq, which allows for better evaluation of the zoonotic risk potential to the Iraqi people and deployed military personnel by feral cat colonies.