Background <p>The interest in the NK genes, a group of conserved homeodomain encoding transcription factors, has increased significantly in the recent years, especially among arthropods and their closest relatives. One reason is that these genes have important and (often) conserved functions in development. Another reason is that some NK genes are clustered within the genomes of different species of arthropods and indeed animals in general. The fact that this clustering has been retained for hundreds of millions of years strongly implies a biological function, and it is believed that shared cis-regulatory elements (CREs) could act to constrain the clusters. Our knowledge about the expression and function of clustered NK genes, however, is still restricted to only a few well-investigated members of this group of genes, while others have only been studied in few model species, or have been completely neglected. Recently, genomic data have provided exciting new insights into the content and clustering of NK genes in non-model species, but corresponding gene expression data are still incomplete or lacking altogether.</p> Results <p>Here we present a comprehensive overview of the complement and embryonic expression pattern of NK genes in a variety of arthropod species and an onychophoran in order to gain further insight into conserved and divergent patterns of NK gene expression which we use to extrapolate the putative ancestral function(s) of these genes in panarthropods.</p> Conclusions <p>We report unexpected instances of expression-pattern swapping among closely-clustered NK genes that may result from CRE-shuffling. We also discuss and conclude on the clustering and order of NK genes in the last common ancestor of bilaterian animals. Finally, we come to the conclusion that NK genes are not just involved in mesoderm evolution but are found to have conserved functions in all germ layers.</p>