To add data on trace metal contamination of Humboldt penguins in the South Pacific, levels of trace metals (As, Hg, Pb, Cu, Zn, and Cd) and porphyrins (copro-, uro-, and proto-) in excreta of Humboldt penguins that inhabit some important nesting sites on the northern coast of Chile were determined. Fresh excreta were collected on Pan de Azúcar Island, Chañaral Island, and Cachagua Island, from December 2011 to January 2012. Concentration of metals was determined by flame atomic absorption spectrophotometry, whereas porphyrins levels were measured by fluorimetric analysis. Concentrations (dry weight) of Cu (199.67 μg g(-1)), As (7.85 μg g(-1)), and Pb (12.78 μg g(-1)) were higher (p ≤ 0.05) in Cachagua Island. Colonies from Pan de Azúcar Island showed the highest levels of Hg (0.76 μg g(-1)), Cd (47.70 μg g(-1)), and Zn (487.10 μg g(-1)). Samples from Cachagua Island showed the highest (p ≤ 0.05) levels of copro- (2.16 nmol g(-1)), uro- (2.20 nmol g(-1)), and protoporphyrins (2.23 nmol g(-1)). There was a positive correlation between the metals As, Pb, and Cu with uro-, copro-, and protoporphyrins. The results indicated that penguin colonies from Cachagua Island are more exposed to metal contamination than penguin colonies from Pan de Azúcar and Chañaral Islands, thus being more likely to develop certain diseases caused by contamination with metals. Considering biomagnification, the metals detected in the excreta of Humboldt penguins can be a source of contamination from marine environments to terrestrial ecosystems, which could also affect other living organisms.