The imitation switch (ISWI) class of chromatin remodeling ATPase is ubiquitous in eukaryotes. It is becoming clear that these enzymes exist as part of larger complexes and the nature of the associated proteins dictate the function associated with a complex both in biochemical assays and in the cell. Much progress has been made in understanding these relationships in the budding yeast Saccharomyces cerevisiae, containing two ATPases, Isw1p and Isw2p. This has been aided by the ease of genetic manipulation, by a number of systematic screens designed to specifically detect ISWI function and by the plethora of data generated from a number of global screens for function. At present, many functions for yeast Isw1p and Isw2p are related to effects on RNA levels and are associated with the controlled repression of gene expression that crudely fall into three types: displacement of the basal transcription machinery to repress or silence transcription of genes (Isw2 complex and Isw1/Ioc3 complex); control of the activation of expression leading to coordination of transcription elongation; and efficient termination of transcription (Isw1/Ioc4/Ioc2 complex). The latter two functions are regulated by specific phosphorylation of residues within the carboxy terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII). Other functions may relate to the ability of ISWI complex to displace transcription factors or enzymes from the template. Other ISWI-containing complexes that have yet to be characterized indicate that much remains to be learnt about yeast ISWI itself and importantly, how the various forms cooperate with different classes of chromatin remodeling ATPase, complexes containing histone acetylases, deacetylases, methylases and both DNA and RNA polymerases.