Most of the Male Karpaty Mts, which form a geographical connecting link between the Eastern Alps and Western Carpathians, consists of an Early Paleozoic low-grade metamorphic complex intruded by Lower Carboniferous granitoid plutons. Metamorphic recrystallization connected with granite emplacement led to the formation of a crystalline complex metamorphosed under greenschist to amphibolite facies conditions. Major and trace element contents of metabasalts and clastic metasedimentary rocks have been studied in this crystalline complex. Distribution of relatively immobile trace elements (REE, HFSE) was unaffected by metamorphism and reflects original magmatic or sedimentary compositions. Two geochemical types of metabasalts have been indentified in relation to their geological position: (1) metabasalts occurring in association with metagabbros, metadolerites and small amounts of black shales and metacherts are of N-MORB type and (2) small metabasalt bodies in clastic metasedimentary rocks with sporadic carbonates are close to E-MORB/OIT or CT in composition. The clastic sedimentary rocks are represented by alternating metapsammitic rocks with variable admixture of pelitic component and organic matter together with a smaller amount of metapelitic rocks and black shales. Relatively uniform major and trace element distribution in the clastic metasedimentary rocks indicates uniformity of the composition and source area of protolith. The protolith of the metasedimentary rocks were close to greywackes from the ensialic back-arc basin depositional setting, with a source comprising mostly a mixture of acid and intermediate magmatic rocks in the upper continental crust. A new lithostratigraphical division of the Early Paleozoic complex of the Male Karpaty Mts is proposed. We define here two groups: (1) the Pernek Group — a metamorphosed incomplete (dismembered) ophiolite sequence representing a relic of the upper part of the oceanic crust Pre-Lower Carboniferous in age and (2) the Pezinok Group composed of clastic metasedimentary rocks with a small amount of metacarbonates and metabasalts with E-MORB/OIT or CT signature Silurian-Devonian in age which represents a part of the rift basin fill probably inboard of an ensialic island arc. Both groups came into contact during strong shortening and nappe formation processes in the Pre-Early Carboniferous (Upper Devonian?) time.