Neoparamoeba spp. are amphizoic amoebae with the capacity to colonize the gills of some marine fish, causing amoebic gill disease (AGD). Here, the gill tissue transcriptome response of Atlantic salmon (Salmo salar L.) to AGD is described. Tanks housing Atlantic salmon were inoculated with Neoparamoeba spp. and fish sampled at time points up to 8 days post-inoculation (p.i.). Gill tissues were taken from AGD-affected fish and a DNA microarray was used to compare global gene expression against tissues from AGD-unaffected fish. A total of 206 genes, representing 190 unique transcripts were reproducibly identified as up or down-regulated in response to Neoparamoeba spp. infection. Informative transcripts having gene ontology (GO) biological process identifiers were grouped according to function. While a number of genes were placed into each category no distinct patterns were observed. One Atlantic salmon cDNA that was up-regulated in infected gill relative to non-infected gill at 114 and 189 h post-inoculation showed significant identity with the Xenopus, mouse and human anterior gradient-2 (AG-2) homologs. Two Atlantic salmon anterior gradient-2 mRNA transcripts designated asAG-2/1 and asAG-2/2, were cloned, sequenced and shown to be predominantly expressed in the gill, intestine and brain of a healthy individual. In AGD-affected fish, differential asAG-2 expression was confirmed in samples used for microarray analyses as well as in AGD-affected gill tissue taken from fish in an independent experiment. The asAG-2 up-regulation was restricted to AGD-lesions relative to unaffected tissue from the same gill arch, while p53 tumor suppressor protein mRNA was concurrently down-regulated in AGD-lesions. Differential expression of p53-regulated transcripts, PCNA and growth arrest and DNA damage inducible gene-45 (GADD45) in AGD-lesions, suggest a role for p53 in AGD-pathogenesis. Thus AGD may represent a novel model for comparative analysis of p53 and p53-regulated pathways.