In order to examine the input of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDDs/PCDFs) from various airborne sources to environmental sinks, the atmospheric deposition of congener-specific PCDDs/PCDFs was investigated. Homologue and congener profiles of atmospheric depositions were compared with those of sources and environmental sinks to identify the relationship among atmospheric depositions, sources, and environmental sinks. Moreover, factor analysis was used to detect similarities, differences, and relationships of the variations in deposition fluxes among congeners within the same and different homologues. The results showed that the congener profiles of the atmospheric depositions were primarily determined by those of combustion emissions. Several congeners in some specific samples showed higher proportions within each homologue compared with representative depositions. This result can be partly explained by the influence of impurities in herbicides, 1,3,5-trichloro-2-(4-nitrophenoxy) benzene (CNP) and pentachlorophenol (PCP). The congener profiles of combustion emissions, representative depositions, and urban soils were very similar although their homologue profiles varied. This implied that PCDDs/PCDFs in the urban soils originate from the deposition of combustion emissions and that all congeners within each homologue behave identically in air and soil. Although the congener profiles of the representative depositions were different from those of the sediments in Tokyo Bay and the soil of a paddy field, the combination of congener profiles of the representative depositions and of the impurities in herbicides. CNP and PCP, can explain the congener profiles of the sediments and the paddy field. This study showed that congener-specific data are useful for source identification.