The Estonian Precambrian basement is considered as a southern continuation of the Fennoscandian Shield of the East European Craton. Magnetite and sulphide mineralization is historically known in the Jõhvi structural zone, North-eastern Estonia. The mineralized beds are subvertical, with complicated internal structural outlines and a large range of rock types. The newly presented data of 1700 structural measurements and 110 geochemical samples are based on the analysis of two new inclined boreholes drilled in 2019–2020. Magnetite occurs as anhedral grains elongated along the rock fabric, as rounded inclusions in other minerals, or as tiny platelets along grain edges and along cleavage planes of amphibole and biotite. Sulphides are present as pyrite, pyrrhotite in addition to minor chalcopyrite, arsenopyrite and iron arsenide – loellingite, galena and sphalerite. Loellingite and arsenopyrite are commonly related to quartz-feldspar veining. Several samples show elevated Au content (up to 205 ppb), which is often observed in magnetite-sulphide mineralized beds, but sometimes in surrounding garnet gneisses as well. The study reveals unusually high manganese contents of 0.2–13.6 wt% in a number of mineralized samples and occasionally in the surrounding gneisses. The new drill core data support the understanding that the Jõhvi Zone is geologically similar to Bergslagen in Sweden and possibly to Orijärvi in southern Finland.