Multiple occurrences of yolk sac retention prompted a retrospective investigation in a recently formed colony of captive Humboldt penguins (Spheniscus humboldti). Necropsy reports of 141 parent-reared penguin chicks that died between January 2014 and December 2018 were reviewed for evidence of yolk sac retention, defined as the presence of a yolk sac at postmortem examination of a chick aged 7 d or greater, and analyzed by demographic and pathological variables for identification of risk factors. Fifty-nine (65%) chicks that died at age 7 d or greater had a retained yolk sac at postmortem examination, revealing that this was a common condition in penguins in this population. Chicks that retained their yolk sac were also more likely to present with minimal gut contents (P = 0.02), have a prominent bursa of Fabricius (P < 0.01), and be the first chick hatched of their clutch (P = 0.02). Parental experience and age were not predictive of yolk sac retention, but there was a trend for chicks with retained yolk sacs to present with a poorer body condition, reduced weight, and reduced crown-rump length compared to chicks without a retained yolk sac. Histopathological and bacteriological findings of retained yolk sacs were not significantly different from those of chicks under 7 d of age. Although likely to be multifactorial, the association between yolk sac retention and indicators of suboptimal feed intake and growth (empty gastrointestinal tract, poor body condition score, decreased crown-rump length, and decreased weight at death) is hypothesized to be a result of parental neglect, leading to starvation and absorption arrest of the yolk, as previously indicated in broiler chicks.