The distribution of conodonts in the Lower–Middle Ordovician beds was studied in five drill core sections of south-eastern Estonia. Ten conodont zones and six subzones, from the Paroistodus proteus Zone to the Eoplacognathus lindstroemi Subzone, were established. The peculiarity of the studied sequence is that the Volkhov Stage is notably poor in conodonts, in particular Baltoniodus species. Large specimens of Drepanodus arcuatus and Protopanderodus rectus, however, are found in great numbers in the uppermost Volkhov and lower Kunda stages. The deeper shelf conodont faunas recognized in SE Estonia (Central Baltoscandian confacies belt) are compared with shallow shelf faunas of northern Estonia (North Estonian confacies belt).