Chromosomal instability (CIN) leading to aneuploidy is a ubiquitous and early event in the progression of Barrett's oesophagus, but its origins are unknown. Hence, the transcriptional levels of components of the mitotic spindle checkpoint (important in ensuring precise chromosome segregation) were examined in Barrett's lesions and correlated with the degree of aneuploidy present in the tissues. Gene expression levels of the MAD2 and BUB1 mitotic spindle checkpoint genes were assessed in 37 Barrett's patients (with histology ranging from metaplasia to adenocarcinoma) by real-time RT-PCR. In addition, the transcriptional levels of HSP27 were also examined as firstly, its expression is known to be down regulated in Barrett's metaplasia (BM) and thus was included as a positive control for the real-time RT-PCR assay. While, secondly, the expression pattern of this gene during Barrett's neoplastic progression was investigated, as this has not been previously assessed. Both over and under expression of the MAD2 and BUB1 mitotic spindle checkpoint genes were detected at all Barrett's histological stages with no apparent selective trend with neoplastic progression. In addition, no correlation with aneuploidy was established, indicating an alternative mechanism must underlie Barrett's associated chromosomal instability. HSP27 expression was reduced in metaplasia and then significantly increased with progression. Gender-related differences were observed and HSP27 expression was higher in poorly-differentiated adenocarcinomas than in well-differentiated forms. HSP27 transcriptional patterns therefore present potential as a prognostic tool to predict the aggressiveness of oesophageal adenocarcinomas (OA).