With the aim of knowing the distribution of As, Hg, and Se in skipjack (Katsuwonus pelamis, Linnaeus, 1758) and yellowfin tuna (Thunnus albacares, Bonnaterre, 1788) from the Eastern Pacific, elemental concentrations were determined in the muscle and liver; As species were also analyzed in the stomach content. Additionally, health risk for consumers was assessed. For both tunas, levels of As and Se were significantly higher (p < 0.05) in the liver than in the muscle. In K. pelamis, Hg concentrations in the muscle were significantly higher (p < 0.05) than those in the liver. In T. albacares, As, Hg, and Se showed a trend to increase with fish dimensions. Arsenic extractability was better in the muscle than in the liver of both species; in K. pelamis, As species were better extracted than in T. albacares. In both tuna species, the most extractable arsenic was arsenobetaine (AsB) and a minor part was dimethylarsinic acid (DMA). The liver contained mainly AsB with some DMA and arsenocholine (AsC). Hazard indexes (HI) indicated no risk from Hg and Se intake through these tuna species. Considering the individual contribution to the HI, Hg contributed more (80 to 86%) than Se. In the context of health risk, none of the As and Hg values were above the permissible limits; however, two samples of T. albacares (9%) and three samples of K. pelamis (12%) had Se concentrations over the limits. If Hg and Se in the edible portion of tuna are considered under the approach of the HBVSe, tuna consumption is beneficial.