The Punta San Juan Marine Protected Area (PSJ) (15°22′S, 75°12′W) protects key breeding populations of Peruvian pelicans (Pelecanus thagus) and guanay cormorants (Phalacrocorax bougainvillii) within the Humboldt Current Large Marine Ecosystem (HCLME). This project's aim was to define current population health and provide an important baseline for continued temporal monitoring. Samples from 110 cormorants and 45 pelicans were collected for complete blood cell counts, plasma biochemistries, plasma protein electrophoresis, and diagnostic testing for avian pathogens (paramyxovirus types 1, 2 and 3; adenovirus types 1 and 2; reovirus; equine encephalitides [Eastern, Western, Venezuelan]; West Nile virus; avian influenza; infectious bursal disease; Marek disease; encephalomyelitis virus; Mycoplasma gallisepticum; Salmonella pullorum; Chlamydia; and Aspergillus). Results of this health assessment demonstrated a low exposure to common avian pathogens. Evidence of exposure to paramyxoviruses, adenoviruses, and Venezuelan equine encephalitis virus was identified most frequently. Although overall prevalence was low, the detection of these viruses highlights potential susceptibility risks for disease outbreaks in this relatively naïve population that can help guide conservation efforts. Continued monitoring of avifauna health at PSJ is a vital component of protection of the unique HCLME.