Barrett's oesophagus (BO) carries an increased risk of progression to oesophageal adenocarcinoma. Chromoendoscopy with methylene blue (MB) can be used to facilitate identification of BO and target areas for biopsy. If photoexcited, MB can generate reactive oxygen species and genotoxic photodegradation products leading to DNA damage. We have previously demonstrated that levels of DNA damage are increased in BO following MB chromoendoscopy. The aim of this study was to investigate whether DNA damage, as measured by the comet assay, can be minimized during chromoendoscopy by varying MB concentration and light wavelength using an in vitro model. OE33 cells were treated with MB (0.015-15 mM) and exposed to white light (WL). Cells were also illuminated with WL fractions (580-700, 480-580, 350-480, <575, <610 and <688 nm) in the presence of MB. At clinically relevant concentrations, WL illumination of MB (15 mM) caused significant DNA damage in vitro (P < 0.001). Illumination of MB with red light (580-700 nm) also stimulated high levels of DNA damage in OE33 cells (P < 0.001). This effect was not observed with green or blue light. Filtering WL to remove red light wavelengths (>575 nm) reduced DNA damage and apoptosis to control levels in MB-treated cells. In addition, reducing the concentration of MB 10-fold markedly reduced the DNA-damaging effect of MB in vitro. The results show that photoactivation of MB by red light is responsible for the majority of DNA damage. Simple modifications to MB chromoendoscopy, such as filtering out red light from endoscopic WL or reducing MB concentration, are likely to limit DNA damage induced by the procedure.