The requirements for the isolation of Mycobacterium avium subsp. paratuberculosis (Map) may be related to the strain-type [sheep (S)- or cattle (C)-type] and not to the host. The objective of this paper was to estimate and compare strain- and biological sample (faeces or pooled-tissue) – specific sensitivities (Ses) of two solid culture media, Herrold’s egg yolk medium (HEYM) and Lowenstein–Jensen (LJ) medium, for the isolation of Map from Greek dairy sheep and goats. From 400 faecal samples collected from sub-clinically infected sheep and goats of four flocks and from 214 pooled-tissue samples (142 from sheep and 72 from goats) collected, at the abattoir, from >1-year-old routinely slaughtered animals, with gross pathology suggestive of paratuberculosis, we isolated 34 Map strains. Of those, by the IS1311 PCR, 18 were categorized into the C-type and nine into the S-type; seven were not typed. We used a Bayesian approach to estimate the strain-specific Ses. SeHEYM-C-faecal = 17% (95% credible interval: 7, 40) was higher than SeHEYM-S-faecal = 2% (0.3, 11). Also, SeHEYM-C-faecal was higher than SeLJ-C-faecal = 4% (1, 12). In pooled-tissue samples, the strain-specific Ses did not differ between the two media.