We studied morphometric, hematology, and serum chemistry variables in 140 Hawaiian monk seals (Monachus schauinslandi) to establish normal baseline values for these variables among free-living seals. We compared seals at French Frigate Shoals (FFS), Midway Atoll (MID), and Pearl and Hermes Reef (PHR) because these subpopulations differ in their rates of population recovery. Dorsal standard length and axillary girth differed significantly between immature (1–4 yr old) and adult (≥5 yr old) seals among sex and island subgroups. Immature seals at FFS were shorter than those at MID and PHR; adult seals at FFS had smaller dorsal standard lengths and axillary girths compared to the other subpopulations. The differences in size were more pronounced among adult females. Significant differences were also found for hematology and serum chemistry variables among seals at FFS, MID, and PHR. Monk seals at FFS had an absolute lymphopenia and eosinopenia compared to those at MID and PHR, compatible with a stress response. Seals at FFS also had lower blood urea nitrogen than seals at PHR, and a lower plasma potassium than seals at MID or PHR. Monk seals had an absolute and relative eosinophilia compared to previously published values. Analysis of subpopulation differences is useful for population health assessment and for long-term monitoring of an endangered species.