The dataset comprises data on the lipid composition (carboxylic acids and alkanols) and stable isotope values (δ13C and δ15N) obtained from fresh stomach oils and sub-stomach oil deposits of snow petrels (Pagodroma nivea). The samples were collected in different un-glaciated regions of East Antarctica (Dronning Maud Land, Mac. Robertson Land, Prince Charles Mountains and Windmill Islands). The stomach oils and sub-fossil stomach oil deposits were analyzed to investigate the paleodiet of the birds and to relate information of paleodiet to past environmental conditions. The alkanoic acids and alkanols were analysed from total lipid extracts by capillary gas chromatography with GC-FID (Gas chromatograph with Flame ionization detector) and GC-MS (single quadrupole mass spectrometer coupled with gas chromatograph). Total lipid extracts were analysed for the δ13C isotopic composition. The un-soluble residues, retained after lipid extraction, was analysed for δ13C and δ15N isotopic composition. This work was funded by the Deutsche Forschungsgemeinschaft (DFG) in the framework of the priority program “Antarctic Research with comparative investigations in Arctic ice areas” (grants BE 4764/5-1 and BE 4764/6-1).