In this study the following methods for the diagnosis of Lawsonia intracellularis infection in pigs were compared in relation to a reference method (examination of ileal mucosal scrapings by the polymerase chain reaction [PCR]): Warthin-Starry (WS) staining of tissue sections, immunohistochemistry (IHC), in-situ hybridization (ISH), and PCR examination of faeces and of paraffin wax-embedded samples of ileum. Of 204 pigs examined, 32 were considered on the basis of the PCR to be infected. Gross and histopathological examination, including the use of WS staining, were of limited value. PCR examination of faeces proved to be the most sensitive (sensitivity 70%) of the methods used but, due to the occurrence of false positives, its specificity (95%) was the lowest. IHC (sensitivity 66%, specificity 99%) and ISH (sensitivity 54%, specificity 100%) were clearly superior to examination of WS-stained sections (sensitivity 34%, specificity 100%) for routine diagnosis; although less sensitive than the PCR, they indicated only cases of clinical relevance and, moreover, were capable of distinguishing different stages and levels of infection. Because examination of paraffin wax-embedded tissue by the PCR was shown to be associated with low sensitivity (41%), IHC was regarded as the method of choice for retrospective studies.