Lower airway inflammation is a frequent cause of poor-performance in horses. An association between inflammation and bacterial isolation in tracheal wash fluid has previously been found; bacterial counts were nevertheless not defined. The aims of this study were to qualitatively and quantitatively compare tracheal bacterial flora of French Trotters with tracheal inflammation (SIT) and control horses (CTL), and evaluate association between endoscopic, cytological and microbiological evaluation of the trachea. Neutrophil percentage in tracheal wash was significantly different between groups whereas tracheal mucus accumulation was not. No significant difference was found between groups for neither percentage of respectively sterile samples or percentage pathogenic bacteria being isolated. Bacterial counts in SIT group were however 10 to 200 times higher than in the CTL group. This study suggests that isolation of pathogenic bacteria alone do not allow estimation of the level of airway inflammation; whereas severe tracheal inflammation may be present in absence of any bacteriological infection.