Paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis, a suspect causative agent of Crohn's disease in man, is an emerging disease of international proportions affecting all ruminants. Early stage detection of Mycobacterium avium subsp. paratuberculosis infection would accelerate progress in control programmes. Despite new molecular approaches the standard diagnostic test for this disease is at present still the time consuming classic isolation procedure. Therefore, alternative diagnostic tests such as PCR, are needed for quick detection of infected animals. In this study, the conventional enrichment and isolation procedure and two IS900-based PCR methods for detection of Mycobacterium avium subsp. paratuberculosis in clinical samples from zoo animals and cattle were compared. A total number of 48 different clinical specimens obtained from animals suspected of having paratuberculosis were examined. The samples included faeces (n = 15) and organ tissues (n = 33). Of the faecal specimens two were identified as positive by nested PCR, whereas none was positive by single PCR or by culture. 28 organ specimens were found positive by culture. Mycobacterium avium subsp. paratuberculosis DNA was detected by nested PCR in 82% of the organ specimens identified positive by culture (23 samples) as opposed to 57% by single PCR (16 samples). Nested PCR also identified two positive samples that were not detected by either culture or single PCR. These findings show the great potential of nested PCR as a useful tool for the rapid diagnosis of paratuberculosis in animals.