The biochemistry of marine mammal blubber differs vertically from skin to muscle, which forms a challenge for using fatty acids (FAs) from differently sampled blubber as a proxy for dietary studies required for ecosystem-based management of coastal resources. In the blubber of some phocid seal individuals, the vertical stratification of several FAs is pronounced whereas in others the FAs distribute almost evenly through the blubber column. Using gas chromatography, we analysed the blubber vertical FA profiles of 30 adult male grey seals from the Baltic Sea, and examined which factors induced the largest vertical change of FA composition detected at the depth of 15–18 mm (outer and middle blubber boundaries). It was revealed that the degree of this compositional shift did not depend on the blubber thickness. Seal age only affected the vertical distribution of the FAs 16:0 and 16:1n-7. However, the outer blubber ratio of ∆9-desaturated monounsaturated FAs (MUFAs) to their saturated FA (SFA) precursors was not increased by grey seal age, contrasting earlier findings for ringed seals. A major determinant of the degree of FA stratification between the outer and middle blubber was the mismatch between the individually varying FA composition of the innermost blubber, regarded to reflect the dietary FA supply the most, and the uniform FA composition of endogenously regulated MUFA-rich outer blubber. Thus, discarding a fixed-depth layer of the grey seal outermost blubber, which we here show to span 0–18 mm from skin and which to a lesser extent reflects the diet of the individual, may in the case of small pinnipeds improve the sensitivity of the FA analysis in assessing spatial, temporal and individual dietary differences. When studying the outer blubber samples using only the diet-derived PUFA variables (SFAs and MUFAs omitted), the sensitivity of the analysis was better than when using this sample type with all main FA variables included.