Vaccination of Atlantic salmon parr with oil-based vaccines will inevitably cause inflammation at the site of injection. albeit the underlying mechanisms are not very well understood or studied in any detail, Here, we report time-course changes In expression levels. assessed by real-time RT-PCR of 1L-1 beta, Mx, two beta-2-microglobulin variants and MHC class 11 beta, front 2 to 19 days post vaccination with a multi-component oil-adjuvanted vaccine. Highly variable individual responses to vaccination make selection of high responders essential prior to subtractive analysis. Based on the above mentioned expression profiles, high-responding individuals at 2.8 and 19 days post vaccination. were selected for subtractive analysis. Clustering of clones according to putative function, sugggest in initial up-regulation of genes involved in metabolism and cell signalling, before onset of genes involved in inflammation. The lag-time forgeries considered as inflammatory markers was more than 48 h, while they were found to constitute the major part of up-regulated transcripts by 8 days post vaccination. fly day 19, immune-related genes like immunoglobulin and T cell-receptor genes, comprised a higher proportion of the up-regulated genes than at earlier time points. (c) 2005 Elsevier Ltd. All rights reserved.