The Itajaí-Açu estuarine system, located in southern Brazil, has great economic importance due to the presence of two ports (Itajaí and Navegantes). This system is affected by industrial and dredging activities, which can cause the remobilization of pollutants accumulated over time in the sediment. In this context, hydrocarbons were assessed in twelve surface sediment samples. n-Alkane and polycyclic aromatic hydrocarbons (PAH) concentrations were determined by gas chromatography and their sources assessed. Total concentrations ranged between 0.50 ± 0.04 and 69.70 ± 3.90 μg g-1 dry weight (d.w.) for n-alkanes and from 63.9 ± 12.1 to 1459.0 ± 43.5 ng g-1 d.w. for PAH. Most of the sediment samples presented carbon preference index (CPI) values close to unity, indicating that the area is submitted to petroleum-related sources, mainly close to Itajaí harbor, where an intense unresolved complex mixture (UCM) was observed. The presence at all stations of αβ-hopane biomarkers also indicated petrogenic input. Based on selected PAH ratios, the sedimentary PAH composition reflects a mixture of both petrogenic and pyrolytic sources. A comparison of the PAH concentrations found in this study with those listed in the sediment quality guidelines (SQGs) indicated that adverse biological effects on the biota are rarely expected.284603614