Information on stress, reproductive fitness, and health is difficult to obtain in wild cetaceans but critical for conservation and management. The goal of this study was to develop a methodology requiring minimal blubber mass for analysis of reproductive and stress steroid hormones and, hence, suitable for cetacean biopsies. Blubber biopsies and samples were collected from free-ranging and stranded gray and fin whales. Steroid hormones were extracted from blubber samples as small as 50 mg using liquid-liquid extraction methodology developed to handle the high fat content of blubber. Samples were analyzed via liquid chromatography with tandem mass spectrometry for 10 hormones: aldosterone, androstenedione, cortisol, cortisone, corticosterone, 17β-estradiol, estrone, 17α-hydroxyprogesterone, progesterone, and testosterone. As part of the optimization, homogenization via bead beating and blade dispersion were compared, and the former found superior. To investigate optimal yet minimal tissue mass required, hormone panels were compared among paired 50, 150, and 400 mg samples, the latter two being commonly reported masses for hormone blubber analysis. Results indicated that 50 mg of blubber was suitable and sometimes superior. Additionally, significant differences in precision values were observed between species, possibly stemming from differences in blubber composition, and relevant to homogenization technique selection and calibration methods that use blubber matrix matches obtained from a species other than the study species. Based on recovery and precision values, our methodology was accurate and precise in the measurement of spiked known quantities for all 10 hormones, confirming the methodology capabilities in 50 mg blubber mass in both species. Altogether, and in our specific sample sets, all endogenous hormones, except corticosterone, were identified above the detection limit in 50 mg gray whale blubber samples while all endogenous hormones, except aldosterone, cortisone, estrone, and progesterone, were detected in 50 mg fin whale blubber samples. We present a robust methodology for the analysis of multiple reproductive and stress steroid hormones in minimal masses of cetacean blubber compatible with small biopsies. Finally, we identified statistically significant differences in corticosteroid concentrations between stranded and free ranging animals.