Saint-Genis-Pouilly is a commune in the Ain department within the Auvergne-Rhône-Alpes region of eastern France.

It is located in the Pays de Gex, at the foot of the Jura Mountains. Bordering the Swiss frontier, it is part of the cross-border area of Geneva. With a population of almost 14,000 inhabitants (2019), it is the fifth most populous commune in the department of Ain.

A large portion of CERN, the European laboratory for particle physics, is located within the territory of Saint-Genis-Pouilly; the ALICE experiment is located on the periphery of the town, and the main entrance to the primary CERN campus (Meyrin) and the ATLAS experiment are located only 3 km from the centre of St Genis. CERN is the world's largest fundamental physics research laboratory and its presence has largely been responsible for the development of the community of Saint Genis since the middle of the 1960s.

Saint-Genis-Pouilly is composed of two market towns (Saint-Genis and Pouilly) and two hamlets (Pregnin and Flies). The two market towns have both continued to expand and now practically merge into one, however the two hamlets still remain separate from each other and from the two towns. The elevation of the commune varies from 419 m (at the extreme south of the commune, to the confluence of the rivers Allondon and Nant de l'Ecra) to 502 m (at the extreme north of the commune, in the village of Flies). The commune is situated at the limit between the plains surrounding Geneva and the first foothills of the Jura. As indicated on the map opposite, the communes surrounding Saint-Genis-Pouilly are: Thoiry, Sergy, Crozet, Chevry, Prévessin-Moëns and Satigny (Swiss).

Many water courses traverse or border Saint-Genis-Pouilly: Lion, Allondon, Nant de l'Ecra, Bief de la Janvoin, Ouaf, Grand Journans and Petit Journans. In 2005 and 2006, these water courses were subject to a ban on water extraction as a result of the drought. In 2004, only the Allondon and the Lion would have been restricted. The depth of the Allondon is measured at Saint-Genis-Pouilly by a network HYDRO station which transmits these readings by telephone.

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