The exposure of marine mammals to the toxins associated with harmful algae can be lethal. Domoic acid (DA) is a biotoxin produced by the Pseudo-nitzschia group of diatoms many of which are now a common component of the Scottish phytoplankton community (Stobo et al., 2008). DA is a potent excitatory neurotoxin that has caused large-scale mortality of marine mammals. We found harbour seals (Phoca vitulina) in Scotland are exposed to DA. Low levels, likely from recent exposure, were measured in the faeces and urine of live captured adult animals (using a direct competitive enzyme linked immunosorbent assay) and exposure was highest during August–September 2008 (7/32 of the faecal (22%) and 11/29 (38%) of the urine samples were positive). Median concentrations in positive faeces and urine were 25ng/g and 6ng/ml respectively. One positive pregnant female was subsequently found dead with 10ng/ml DA in her amniotic fluid but the contribution of DA exposure to the cause of death could not be established. However, the highest levels in the study were found in anonymous faecal samples collected in September 2009 on the east coast of Scotland (up to 397ng/g). Further studies are urgently needed to determine the importance of DA exposure to the population dynamics of Scottish harbour seals in light of the recently reported major population declines.