Serum paraoxonase (PONI) is responsible for the metabolism of organophosphates in serum, and PONI activity is a major determinant of their toxicity in humans. There have been reports linking lowered PONI activity to physical symptoms after deployment to the Persian Gulf War (PGW) of 1990 to 1991. Therefore, the object of this study was to determine (1) whether PONI activity was decreased among symptomatic PGW veterans compared with asymptomatic PGW veterans and (2) to determine whether PGW veterans as a whole had lower PONI activity compared with other military control groups. This was a case control study nested in occupational cohort study of military personnel. Four groups of military personnel were identifted from a large epidemiological study of health effects of deployment to the PGW and Bosnia: (1) symptomatic PGW veterans, n = 115; (2) healthy PGW veterans, n = 95; (3) symptomatic Bosnia peacekeeping veterans, n = 52; and (4) symptomatic nondeployed military controls, n = 85. The main outcome measures were PONI activity and genotype for PONI-55 and -192. We found significant difterences in PONI activity among these four groups, and although the two Gulf groups did not differ in PONI activity, those deployed to the Gulf had significantly lower PONI activity compared with the non-PGW groups (median difference = 70.9; 95% CI: 20.2, 121.5, P = 0.012). These differences were not explained by a range of potential confounders, or differences in PONI coding region polymorphisms. PONI activity is reduced in PGW veterans compared with military control groups. The effect is independent of ill health in PGW veterans.