Respiratory tract disease is the second most common cause of poor performance in racehorses after musculoskeletal disease. Lower respiratory tract disorders (LRTD) are common in thoroughbred horses of all ages. The aim of this study was to investigate whether there was any association between the microbiological and cytological examinations. Fifty horses ranging in age from 2 to 6 years were examined. Horses with only upper respiratory tract abnormalities identified by endoscopy (at rest) were eliminated from the study and horses with LRTD were used in this study. Tracheal aspirate specimens were collected for cytological and microbiological examinations. Thirty six horses had positive and 14 horses had negative cultivation. The isolated bacteria included 13-haemolytic Streptococcus equi subsp. zooepidemicus (38.8%), Escherichia coli (22.2%) and other bacteria that were isolated at rates ranging from 0.4 to 1.8%. Percentages of neutrophils, lymphocytes, eosinophils, macrophages and mast cells were evaluated in the cytological examination. The percentages of neutrophils were significantly higher in the samples with isolated bacteria (35.75 +/- 2.60%) compared to the samples from which bacteria were not isolated (16.79 +/- 2.36%) (P < 0.001). This study shows that S. equi subsp. zooepidemicus could play an important role in the etiopathogenesis of LRTD. It also demonstrates the importance of evaluating the microbiological findings of the tracheal aspirate specimens from horses suffering from respiratory infections, in addition to performing a detailed clinical examination and other complementary tests that focus on the respiratory system, such as endoscopy and cytology of the tracheal aspiration.