The upper and lower respiratory tracts of 59 feedlot calves with clinical signs of naturally occurring respiratory disease (cases) and 60 comparison (control) animals were cultured before treatment, using nasopharyngeal swabs (NPS) and bronchoalveolar lavage (BAL). The most prevalent organisms were Pasteurella multocida and Mycoplasma bovis. Isolations of P. multocida from NPS and BAL fluid were found to be significantly associated with morbidity (p less than or equal to 0.05), but the frequency with which other organisms were isolated from the nasopharynx and lungs was similar in cases and controls. There was evidence of moderate agreement between NPS and BAL isolates at the individual calf level using the kappa statistic, (range of kappa values = 0.47-0.61) but the variability of the kappa statistics was large. Therefore, in an individual calf NPS cultures did not accurately predict BAL cultures. The NPS and BAL culture results were quite similar at the group level, however.