Livestock manures and composts can be contaminated by Mycobacterium avium subsp. paratuberculosis (MAP) which can cause paratuberculosis - Johne's disease, an intestinal infection of domestic and wild ruminants. Therefore the inactivation of inoculated MAP ATCC 43015 in the compost and in the manure in storage was carried out. MAP (2.0 x 10(6)/g) was inoculated into the compost in three actively ventilated and isolated vessels and in a conventional manure storage pile. Herrold's Egg Yolk medium with supplements for MAP growth, followed by IS900 PCR for isolate identification was used. Direct PCR assessment of the persistence of sequence IS900 in the compost and manure material in parallel was implemented. Moisture, ash and ammonia content in the compost and manure specimens were determined and pH was measured. Salmonella enterica serovar Senftenberg (S. Senftenberg) was introduced into the compost and manure materials to demonstrate the hygienisation process. The presence of MAP on the culture media was confirmed in the samples 16 and 24 hours after exposure in compost and manure, respectively. No MAP was isolated on the medium after 24 hours of exposure. However, using the PCR assay of compost specimens, persistence of MAP was proved in the compost samples until day 7 and in the manure in storage even after 21 days of exposure. S. Senftenberg S-73/98 was not present 24 hours after exposure either in compost or manure storage.