Computing for ATLAS in Switzerland has two Tier-3 sites with several years of experience, owned by Universities of Berne and Geneva. They have been used for ATLAS Monte Carlo production, centrally controlled via the NorduGrid, since 2005. The Tier-3 sites are under continuous development. In case of Geneva the proximity of CERN leads to additional use cases, related to commissioning of the experiment, which require processing of the latest ATLAS data using the latest software under development, normally not distributed to grid sites. The Swiss Tier-2 at the CSCS centre has a recent and powerful cluster, serving three LHC experiments, including ATLAS. The system features two implementations of the grid middleware, NorduGrid ARC and the LCG gLite, which operate simultaneously on the same resources. In this article we present our implementation choices and our experience. We will discuss the requirements of our users and how we meet them. We will present the status of our work and our plans for the ATLAS data taking period in 2009-2010.