IgA is the predominant immunoglobulin class in mucosal secretions and secretory deficiencies may predispose to chronic enteropathies. The polymeric immunoglobulin receptor (pIgR) facilitates the transport of IgA across the epithelial border. Critical to the transport of IgA by pIgR is the presence of a polypeptide joining chain (J-chain) linking the IgA monomers of the dimeric IgA molecule. In this study we examine the difference in expression of mRNA transcripts for pIgR, alpha-chain and J-chain by real-time reverse-transcription polymerase chain reaction (RT-PCR) in endoscopic biopsies from the duodenum of dogs with and without chronic diarrhoea. One-step, real-time RT-PCR was used to quantify the level of expression of transcripts for the housekeeper gene G3PDH, pIgR, alpha-chain and J-chain. There was no significant difference in expression of any transcript between dogs with (n=11) and without (n=8) chronic diarrhoea. Expression of alpha-chain mRNA in both groups had a similar bimodal distribution, as individuals either expressed relatively 'high' or 'low' levels of this transcript. The secretion of IgA by plasma cells is under the control of Th-2 cytokines, therefore the finding of 'high' and 'low' levels of alpha-chain expression may reflect different levels of these cytokines in duodenal mucosa.