Ocean acidification (OA), the process by which increasing atmospheric CO2 is absorbed by the ocean, lowering the pH of surface waters, has been shown to affect many marine organisms negatively. It has been suggested that organisms from regions with naturally low pH waters, such as upwelling areas, could serve as models for future effects of OA and may be adapted to increased pCO2 levels. In this study, we examined the effects of OA on yellowfin tuna, a highly pelagic species that spawns in the eastern tropical Pacific, an area that includes regions of strong upwelling events. Larvae reared at decreasing pH levels (pH 8.1, 7.6, 7.3 and 6.9) showed increasing organ damage in the kidney, liver, pancreas, eye and muscle, which correlated with decreased growth and survival. These findings complement earlier studies on organ damage in Atlantic cod and herring larvae and demonstrate that OA may have detrimental effects on fish larvae, regardless of their pre-exposure to low pH waters.