The scope of this work was to evaluate the levels of polycyclic aromatic hydrocarbons (PAHs) and their possible sources in two shallow sediment cores from an estuarine area located in the south region of Brazil, the Guaratuba Bay. The estuary is encompassed by an Environmental Protection Area (EPA) of 1306 km 2, which is still considered to be pristine, despite recent urban growth. To assess levels of 14 selected PAHs in the sediments, among those listed as “priority pollutants” by the US Environmental Protection Agency, the cores were divided in several sections, followed by extraction, clean-up, fractionation and subsequent analysis using HPLC coupled to a fluorescence detector. Among the PAHs detected, phenanthrene and fluoranthene showed the highest concentrations. PAHs with more than four rings were usually present in low concentrations or were undetectable. To assist in the identification of possible sources, the ratios An/(An + Phe) and Flt/(Flt + Py) (anthracene to anthracene plus phenanthrene and fluoranthene to fluoranthene plus pyrene) and a PCA model were also used. Total concentrations of PAHs ranged between 1.5 and 3130 ng/g (mean 495) dry weight for the core collected in the inner part of the estuary, and between 78.5 and 3270 ng/g (mean 899) dry weight for the other core, collected in the outer part. Compared to values found in other studies in coastal zones along South American eastern margin, this area can be considered to range from low polluted to moderately polluted. From the data, it was also possible to conclude that there is predominance of petroleum sources, and essentially close to the more urbanised areas. Combustion sources have only minor contribution and are episodic, when compared to the latter.