- Skin condition assessment of wildlife can provide insight into individual and population health. Yet, logistics can limit skin condition assessment of large whales. We developed a standardized, quantitative protocol using photographs to assess skin condition of blue whales in New Zealand, and demonstrate the value gained by testing hypotheses, documenting new morphologies, and establishing baselines that can be monitored for change. We reviewed a photo-identification catalog to compile common markings, categorized markings according to existing definitions, and described markings not previously documented. Photographs of blue whale skin (n = 1,466) were assessed to quantify marking prevalence, severity, and co-occurrence patterns. Of the whales assessed (n = 148), 96.6% had cookie cutter shark bites, 80.4% had blister lesions, 56.0% had pigmentation blazes on the dorsal fin, and 33.7% had holes in the dorsal fin. Additionally, 35.8% had “starburst” lesions, a previously undocumented marking. Blister and cookie cutter shark bite severity did not accumulate linearly, indicating that the two marking types are unrelated. There was a positive relationship between blister severity and number of starbursts, indicating that the two could be related; based on morphological similarities, starburst lesions may derive from ruptured blisters. Whales with holes in their dorsal fin had significantly higher blister severity than those without, indicating that these markings could be related; this is supported by observed blisters on dorsal fins of blue whales. There was a significantly higher probability of fresher cookie cutter shark bites on whales observed at more northerly latitudes, but no relationship between blister severity or number of starbursts and latitude. These latitudinal patterns indicate that blue whales in New Zealand accumulate cookie cutter shark bites at more northerly latitudes; this finding is supported by the known range of cookie cutter sharks in New Zealand waters. Of the eight individual whales re-sighted across multiple years, there was no uniform pattern in lesion change over time, however, individual cases revealed lesion healing over a multi-year timeframe. Our protocol for quantifying skin condition can be applied to any cetacean photo-identification catalog, and can be used to compare across individuals and populations, and explore causal links between skin condition and cetacean health.