Stable isotope analysis (SIA) of free-swimming mysticetes using biopsies is often limited in sample size and uses only one sample per individual, failing to capture both intra-individual variability and the influence of demographic and physiological factors on isotope ratios. We applied SIA of δ13C and δ15N to humpback whale (Megaptera novaeangliae) biopsies taken during the foraging season along the western Antarctic Peninsula to quantify intra-individual variation from repeatedly sampled individuals, as well as to determine the effect of biopsy collection site, sex, and pregnancy on isotope ratios. There was substantial variability in δ13C from multiple biopsies taken from the same individuals, though δ15N was much more consistent. Side of the body (left versus right) and biopsy location (dorsal, anterior, ventral, and posterior) did marginally affect the isotopic composition of δ15N but not δ13C. Pregnancy had a significant effect on both δ13C and δ15N, where pregnant females were depleted in both when compared to non-pregnant females and males. These results indicate that isotopic signatures are influenced by multiple endogenous and exogenous factors and emphasize value in accounting for intra-individual variability and pregnancy status within a sampled population. Placed within an ecological context, the endogenous variability in δ13C observed here may be informative for future isotopic analyses.