An integrated study of the litho-, bio-, and isotope stratigraphy of carbonates in the Southern Alps was undertaken in order to better constrain δ¹³C variations during the Late Carboniferous to Late Permian. The presented high resolution isotope curves are based on 1299 δ¹³C_carb and 396 δ¹³C_org analyses. The carbon isotope record of diagenetically unaltered samples from the Carnic Alps (Austria) and Karavanke Mountains (Slovenia) shows generally high δ¹³C values, but Late Carboniferous and Early Permian successions are affected by a diagenetic alteration as consequence of glacio-eustatic sea level changes. Negative δ¹³C excursions are related to low-stand deposits and caused by diagenetic processes during subaerial exposure. The comparison with δ¹³C records from other parts of the world demonstrate that δ¹³C values are high in most unaltered samples, an overall negative trend during the Permian, as recently published, is not obvious and negative excursions related to changes in the carbon isotope composition of the global oceanic carbon pool cannot be confirmed, except for the Permian–Triassic boundary interval.