Marine sediment contamination was evaluated in a set of sediment specimens collected from Izmir Bay (Turkey) and from Mytilene Harbor (Greece) in the Aegean Sea. Eight sediment specimens from Izmir (#IZ to #IZ8) and seven sediment specimens from Mytilene (#MYT1 to #MYT7) were analyzed for their content in different classes of contaminants, i.e. inorganics, organic carbon (OC), and seven polycyclic aromatic hydrocarbons (PAHs). Significantly higher levels of inorganic contaminants were detected in Izmir vs. Mytilene sediment, and the highest inorganic contamination was detected in the innermost sampling sites in Izmir Bay, namely sites #IZ1 to #IZ4. This was the case for Al, As, Cr, Cu, Fe, Li, Mn, Pb, Ti and Zn. Granulometric analysis, OC and individual PAH congeners failed to show any significant differences between total Mytilene and total Izmir Bay sediment samples. Nevertheless, the sum of PAHs in sites #IZ2 to #IZ4 displayed significantly higher levels both vs. the other Izmir sites and vs. all Mytilene sediment samples. The overall results point to higher pollution status in Izmir Bay, especially in the innermost sampling sites, compared to Mytilene Harbor, detected as inorganic contamination and as PAH contamination in some Izmir sampling sites.