The epidemiology of bovine herpesvirus type 1 (BHV-1) and bovine viral diarrhoea virus (BVDV) was studied in a population of small dairy herds that had not been vaccinated. Bulk tank milk samples of 186 herds in Thailand were collected four times between 2002 and 2004. Serum samples from individual animals in 11 herds were also taken on three occasions. The prevalence of BHV-1 in the 186 herds was 61% in 2002, decreasing to 48% in 2004 and for BVDV was 91% in 2002, decreasing to 72% in 2004. A BVDV antigen-positive calf was found in one of the 11 herds, and animals in this herd and three other herds seroconverted to a recently described atypical BVDV strain (HoBi). This study showed a significantly decreasing prevalence for both BHV-1 and BVDV due to a self-clearance process. Further studies are needed to find out how the atypical BVDV strain entered the cattle population.