Harbor Seals (Phoca vitulina) are the most common and widely distributed pinniped in Washington State coastal waters. Serving as sentinels of marine ecosystem health, stranded animals are useful in detecting environmental disease and contaminant levels. From 2004 to 2010, we examined mortality rates and causes of death of Harbor Seal pups at Smith Island, a principal haulout site in the eastern Strait of Juan de Fuca, Washington, conducting 21 site surveys during the pupping season (June through August). We documented and externally examined 245 dead pups and of these, 72 were deemed suitable for more detailed internal examination and were collected for necropsy to determine cause of death. Minimum estimated neonatal mortality varied widely by year and ranged from 3 to 25%. The highest number of dead pups, nearly half of the total for the study, were found in 2005; this was also the year with the highest estimate of pups born and highest proportion of pups born that were documented dying. Infection was the leading primary cause of death in most years including 2005, when 40% of the pups died from an infectious process. The 2nd leading cause of death was malnutrition; other causes included prematurity and dystocia. This study documents some of the major annual differences that can occur in both mortality rates and causes of death in Harbor Seals.