In order to investigate the role of infectious agents in the aetiology of lower respiratory tract disease in Thoroughbred racehorses, a matched case-control study was conducted. Cases were identified by the presence of coughing, and were compared to a control population matched on time of sample collection and location within the same training establishment. Tracheal wash samples were collected from 100 cases and 148 controls. Case horses were more likely than controls to have endoscopic and cytological evidence of airway inflammation. There was no significant association between serological evidence of infection by commonly implicated respiratory viruses and coughing. Similarly, mycoplasma were rarely isolated and were not associated with disease. In contrast, there was a strong association between isolation of greater than a total of 103 colony-forming units/ml of tracheal wash and coughing. Individual bacterial species associated with disease included Streptococcus zooepidemicus, Streptococcus pneumoniae, Streptococcus suis, Streptococcus sanguis, Pasteurella spp and Bordetella bronchiseptica. This study provides evidence of the role of bacterial infection in the aetiology of lower respiratory tract inflammation in racehorses. However, in 58% of cases, few or no bacteria were isolated. Hence, at the time of identification of disease, there was no evidence of viral, bacterial or mycoplasmal infection in the majority of coughing horses. The aetiology of the signs observed in these horses requires further investigation.