Identification of individual animals is important in order to evaluate age-specific survival rates, onset of sexual maturity and reproductive rates in wildlife populations. Of the various methods available to researchers, hot branding is the most effective, although somewhat controversial, tool available. The physiological effects of hot-iron branding (n = 7) were assessed using temporarily captive juvenile Steller sea lions (Eumetopias jubatus) (n = 22). Sea lions showed statistically significant increases in white blood cell count, platelet levels, globulin and haptoglobin concentration up to two weeks after branding. No significant differences were found in serum cortisol levels. The changes in health parameters we saw after branding were consistent with minor tissue trauma and indistinguishable from baseline levels after 7–8 weeks.