Q fever is a zoonotic illness which frequently has a non-specific clinical presentation. Cases among deployed US military personnel have been reported in increasing numbers indicating an emerging at-risk occupational group. Banked serum specimens were utilized to estimate seroprevalence and risk factors among military personnel deployed to Iraq. Coxiella burnetii antibody testing was performed and epidemiologic data were analysed from 909 servicemembers. The overall number who seroconverted to Q fever was 88 (10%). The most common ICD-9 code assigned to Q fever cases was fever not otherwise specified (NOS) (45%). A combat occupational specialty was a risk factor for Q fever seroconversion (OR = 1.8, 95% CI: 1.1-2.8) as well as receiving a primary diagnosis of fever NOS (OR = 2.6, 95% CI: 1.6-4.1). These findings indicate that Q fever is a significant infectious disease threat to military personnel deployed to Iraq. A heightened awareness among physicians is necessary to ensure prompt diagnosis and treatment.