Bronchoscopic, endotracheal and transtracheal lung lavage were evaluated in 38 healthy pigs taken from a nucleus herd in a good state of health with respect to their applicability in practice and the traceability of bacteria, cellular parameters and the antimicrobial peptide PR-39 in the respective lavage fluid samples. The total cell count, qualitative morphological cellular characteristics as well as PR-39 could be determined in all lavage fluid samples, while quantitative cell differentiation was not possible in endotracheal lavage samples. The comparison of the three methods resulted in a higher proportion of polymorphonuclear neutrophil granulocytes (PMNs) and higher concentrations of PR-39 in transtracheal samples. For this reason different valuation standards with respect to PMNs and PR-39 concentrations are presupposed for transtracheal lavage samples. The occurrence of pavement epithelial cells as well as the number of contaminating bacterial species per sample was the lowest in transtracheal lavage. Mycoplasma hyopneumoniae polymerase chain reaction appeared to have the highest diagnostic sensitivity in combination with bronchoscopic lavage. In conclusion, bronchoscopic and transtracheal lavage were considered to be more appropriate for bacteriological and cytological diagnostics than endotracheal lavage.