The Drosophila genome contains >13,000 protein coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here we present a genome-wide fosmid library of ≈10,000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins we have created transgenic lines and for a total of 207 lines we have assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we can visualise many proteins at endogenous expression levels and find a large fraction of them localising to subcellular compartments. Using complementation tests we demonstrate that two-thirds of the tagged proteins are fully functional. Moreover, our clones enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will enable systematic analysis of protein expression and localisation in various cellular and developmental contexts.