Introduction In Niamey, Niger, interactions within the interface between animals, humans and the environment induce a potential risk of brucellosis transmission between animals and from animals to humans. Currently, little is known about the transmission of Brucella in this context. Results 5,192 animals from 681 herds were included in the study. Serum samples and hygroma fluids were collected. A household survey enabled to identify the risk factors for transmission of brucellosis. The true adjusted herd-level prevalence of brucellosis ranged between 11.2% and 17.2% and the true adjusted animal-population level prevalence was 1.3% (95% CI: 0.9–1.8%) based on indirect ELISA test for Brucella antibodies. Animals aged of 1–4 years were found to be more susceptible than animals less than 1 year old (Odds ratio [OR] of 2.7; 95% CI: 1.43–5.28). For cattle, the odds of brucellosis seropositivity were higher in rural compared to the periurban areas (OR of 2.8; 95% CI: 1.48–5.17) whereas for small ruminants the risk of seropositivity appeared to be higher in urban compared to periurban areas (OR of 5.5; 95% CI: 1.48–20.38). At herd level, the risk of transmission was increased by transhumance (OR of 5.4; 95% CI: 2.84–10.41), the occurrence of abortions (OR of 3.0; 95% CI: 1.40–6.41), and for herds having more than 50 animals (OR of 11.0; 95% CI: 3.75–32.46). Brucella abortus biovar 3 was isolated from the hygromas. Conclusion brucellosis in Niger is a serious problem among cattle especially in the rural areas around Niamey and among sheep in the urban areas of Niamey. The seroprevalence varies across strata and animal species with important risk factors including herd size, abortion and transhumance at herd level and age at animal population level. For effective control of brucellosis, an integrated approach seems appropriate involving all stakeholders working in public and animal health.