Northeastern Uganda has suffered from protracted armed conflict and HIV/AIDS and has some of the highest rates of intimate partner violence (IPV) globally. Little is known about how exposure to conflict and HIV influence individuals' syndemic risk markers or those of their partners. We conducted a population-based study using multistage sampling across three districts in Northeastern Uganda. We randomly surveyed 605 women aged 13-49 years and estimated syndemic problems for currently partnered women (N = 561) who reported for their male partners. Syndemic problems were lower in the low-conflict district than the high-conflict district, p = .009. Conflict exposure was associated with couples' syndemic scores, respondent: β = 0.182, p < .001; partner: β = .181, p < .001. Problem scores were significantly higher among women whose partner was either HIV positive, p = .031, or had an unknown HIV status, p = .016, compared with those whose partner was HIV negative. The total effects of women's, β = .15, p = .034, and men's, β = .137, p = .038, armed conflict exposure on male-to-female IPV were significant. For male partners, there were significant total effects of having an unknown, β = .669, p < .001, or positive, β = 1.143, p < .001, HIV status on experiencing female-to-male IPV. These results suggest that syndemic problems and corresponding treatments should consider couple influences. Addressing mediating problems of mental distress and alcohol misuse may reduce the risk of male-to-female IPV. Providing couple-based HIV psychosocial interventions could reduce men's exposure to IPV.