The frequent use of perfluorinated chemicals (PFCs) in industrial applications and domestic products has led on a global basis to a continuous detection of PFCs in a wide range of environmental matrices including aquatic systems. Perfluorooctane sulfonate (PFOS) is the most commonly detected PFC in biotic and abiotic samples. To date, the understanding of the potential effects of PFOS towards biological systems has reached substantial progress. However, the majority of studies have focused on acute effects, leaving long-term effects largely unexplored. Given the persistent properties and the reported membrane altering potential of PFOS a long-term assessment in combination with other pollutants should be a promising strategy to shed more light on the complex toxicology of PFOS. Since PFOS has been shown to act as an endocrine disruptor in fish a combined investigation with another endocrine disrupting chemical (EDC) would represent an approach where specific endpoints such as sex steroid levels could be measured and compared, thus providing a more direct hint of any interactive effects. In the present study we investigated waterborne PFOS both alone and in a binary mixture with the known EDC bisphenol A (BPA) over two full generations of the zebrafish (Danio rerio). Survival, growth, reproductive success, vitellogenin (VTG) and histological alterations in thyroid, liver and gonads were examined. PFOS (300 μg/L) was found to induce lipid accumulation in liver of F1 generation fish. A parallel finding in PFOS (300 μg/L) exposed fish was the occurrence of granuloma, presumably as a result of bacterial infection. Identical granuloma structures were detected in lower PFOS concentrations in F2 generation fish, indicating a suppressed immune system over generations. BPA tended to increase plasma VTG concentrations whereas the opposite trend was observed for PFOS. Binary mixtures of the two chemicals indicated no synergistic effects. Conclusively our study does not validate the hypothesis that the presence of PFOS increases the endocrine potential of BPA. However, our results indicate an immune suppressing potential of PFOS which seems to be enhanced over generations.