On June 25–26, 2009 the 5th Workshop on innovative mouse models was held in the Leiden University Medical Center, Leiden, The Netherlands. The primary goal of this two-day workshop has always been to bring together a diverse group of scientists interested in advanced genome alteration approaches in the mouse, including key developers of emerging technologies as well as researchers who wish to apply and assess these new approaches. The workshop encourages an in-depth and unvarnished discussion of these technologies and novel developments in a very open and informal way, easy accessible for young and senior researchers. The organising committee consisting of Jos Jonkers (NKI, Amsterdam, The Netherlands), Paul Krimpenfort (NKI, Amsterdam, The Netherlands), Werner Muller (University of Manchester, UK), Els Robanus Maandag (LUMC, Leiden, The Netherlands), Hein te Riele (NKI, Amsterdam, The Netherlands), Marian van Roon (AMC, Amsterdam, The Netherlands) and Sjef Verbeek (LUMC, Leiden, The Netherlands) all, except for Werner Muller, participated in the group of Anton Berns, NKI, Amsterdam and got acquainted with transgenic technologies and mouse models in his lab. From 2003 onwards they decided to bring together all researchers in these fields in the characteristic informal, but outstanding workshops on IMM. The workshops grew from a European meeting to an international workshop, bringing together 150–200 scientists (see http://workshop.nki.nl). This year, during the first lustrum, topics included: induced Pluripotent Stemcells, Sleeping Beauty transposon mutagenesis, large scale generation of conditional knockouts, in vivo RNAi and mosaic mouse models. The topics were covered during the first day of the workshop by excellent and outstanding keynote speakers, while the second day the same topics were discussed by young scientists in high quality, short presentations.