Differences in risk perceptions of public health and food safety hazards in various poultry husbandry systems by various stakeholder groups, may affect the acceptability of those husbandry systems. Therefore, the objective was to gain insight into risk perceptions of citizens, poultry farmers, and poultry veterinarians regarding food safety and public health hazards in poultry husbandry systems, and into factors explaining these risk perceptions. We surveyed risk perceptions of Campylobacter contamination of broiler meat, avian influenza introduction in laying hens, and altered dioxin levels in eggs for the most commonly used broiler and laying hen husbandry systems in Dutch citizens (n = 2,259), poultry farmers (n = 100), and poultry veterinarians (n = 41). Citizens perceived the risks of the three hazards in the indoor systems higher and in the outdoor systems lower than did the professionals. Citizens reported higher concerns regarding aspects reflecting underlying psychological factors of risk perception compared to professionals. Professionals indicated a relatively low level of personal control, which might imply risk denial. Of the socio-demographic characteristics, gender and childhood residence were associated with risk perceptions. The influence of other factors of risks perception are discussed. It is suggested that risk perceptions of all stakeholder groups are influenced by affect, stigma, and underlying values. To adapt current or new husbandry systems that can count on societal support, views of key stakeholders and multiple aspects such as animal welfare, public health, food safety, and underlying values should be considered integrally. When trade-offs, such as between animal welfare and public health have to be made, insight into underlying values might help to find consensus among stakeholders.