The subject of the study is a brief assessment of the operations of the SS Secret Service – Sicherheitsdienst (SD) in Slovakia during the period of autonomy (October 1938–March 1939), how it interfered with the internal political process and how it was instrumental in Slovak secession and the Nazi plans for the post-Munich Czechoslovakia. The second part of the study is devoted to Werner Göttsch, a member of the “Amt III Ausland” SD, who played a relatively important role in promoting the German scheme in Slovakia in the first quarter of 1939.