Comprehensive congener fingerprints of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), including non-2,3,7,8-substituted congeners, in 142 surface sediment samples from the Baltic Sea were characterized by Principal Component Analysis (PCA). The pattern analysis revealed source specific indicators of chlorophenol use, high temperature processes, chlorine bleach/chloralkali production and a source signature suggested to originate from pulp/paper or related production. Congener patterns in sediments from offshore and pristine coastal areas showed strong resemblance to patterns of atmospheric deposition and flue gases, indicating that these sources have high impact in areas that are not affected by point sources. Prominent contributors to the patterns of hotspot areas along the Swedish coast included chlorophenol indicators and a source characterized by hexa-CDDs while the contribution of the traditional chlorine bleach pattern was weaker. This study demonstrates the importance of comprehensive PCDD/F congener analysis for identifying links to candidate sources.