To determine the levels of background scrapie-like pathology in the brains of clinically normal adult sheep, the brains of 1106 sheep from 28 known scrapie-infected flocks and nine apparently uninfected flocks were examined during 1998 and 1999. One per cent of the brains had vacuolar pathology and disease-specific accumulations of prion protein consistent with a diagnosis of scrapie. All the positive animals had at least one allele of the prion protein gene encoding valine at codon 136, and originated from flocks in which cases of clinical scrapie had been confirmed within the last four years. The parasympathetic nucleus of the vagal nerve was the most consistently and severely affected nucleus in the medulla oblongata, suggesting that the infection enters the brain via ascending fibres of the vagus nerve.