M. a. paratuberculosis strains are divided in two main types, the cattle and the sheep group. The sheep group, characterised by an extremely slow growth, has been described mainly in ovine strains from Scotland, England, Denmark, Australia, Iceland, South Africa, New Zealand, and Canada This type corresponds with the sheep and intermediate group described by IS900-RFLP, and the Type I and III described by PFGE. The objective of this study is to demonstrate that M. a. paratuberculosis strains belonging to the sheep type are common in domestic ruminants in Spain, and probably in the rest of Europe. One hundred and sixty four M. a. paratuberculosis isolates from domestic ruminants (83 goats, 78 cows and 3 sheep) from different Spanish regions were typed with specific PCRs (Whittington et al. 1998; Collins et al. 2002) to distinguish between cattle and sheep types. Surprisingly, 31.7% of the strains belonged to the sheep type (29 cows, 20 goats and 3 sheep) and were characterised by: 1) long incubation period, 46.2% of the strains took more than 5 months to grow; 2) preference for the Löwenstein-Jensen media (55.8%); and 3) difficult to be subcultured and therefore to be characterised by IS900-RFLP and PFGE. Despite this fact, both protocols were applied in some M. a. paratuberculosis strains and results confirm their classification into the sheep group since they were typed as Type III and Intermediate group by PFGE and IS900-RFLP, respectively. These results highlight the fact that it is essential to identify the type of M. a. paratuberculosis strains to guarantee that the diagnosis protocol is appropriate. We recommend the implementation of these PCRs as a routine protocol in paratuberculosis diagnosis, since the presence of sheep type M. a. paratuberculosis strains is a fact that has to be taken into account in control programs.