Due to trade liberalisation with farm animals, paratuberculosis is rapidly spreading among ruminants in many European countries. Two countries with a very different situation are Sweden and the Czech Republic. Sweden has a very low disease prevalence and a limited cattle import and the Czech Republic had a massive cattle import after 1992. Isolates of M. paratuberculosis from the two countries were examined using DNA fingerprinting (restriction endonucleases PstI and BstEII). Thirteen Swedish isolates of M. paratuberculosis from cattle were investigated. Five isolates from animals imported from Denmark (4 Blonde d'Aquitaine, 1 Limousine) and one isolate from a cow imported from Finland (Aberdeen Angus). Six isolates came from herds within a domestic chain of infection, in the Limousine breed, originating from import from France via Denmark in 1975. One isolate came from a Swedish Friesian cow, without any obvious connections to imported animals. All Swedish isolates were of DNA type B-C1. This supporting the infection spread from imported animals to animals originally reared in Sweden. Of 23 cattle herds originally reared in the Czech Republic, strains were of the DNA types B-C9 (6 herds), A-C10 (5 herds), D-C12 (8 herds), E-C1 (1 herd), and B-C1 (3 herds in contact with imported ruminants). In all 34 infected cattle herds (Blonde d'Aquitaine, Charolais, Holstein, Hereford, Jersey, Limousine, Mont Belliarde) imported from Denmark, France, Germany and Hungary, type B-C1 was the most prevalent. In three of these herds, one animal harboured a strain of another type (E-C1, A-C10 and I-C13). Among other ruminants with paratuberculosis, domestically reared sheep harboured types A-C10, A-C8, B-C1, B-C2, and E-C1, goats C-S1 and B-C1 and deer A-C10 and B-C1. In imported wild goats from Estonia type B-C1 was found, in imported goats from Denmark B-C1 and in deer from Scotland B-C16. Research was partially supported by the Ministry of Agriculture of the Czech Republic (grant no. EP0960006087) and the Swedish Council for Forestry and Agricultural Research (grant no. 31.1189/97).