The identity of compounds responsible for estrogenic and dioxin-like activities in sediment from the harbour of the small town Zierikzee in Zeeland, The Netherlands, was investigated using a bioassay directed fractionation approach with the in vitro estrogen and dioxin responsive reporter gene assays ER- and DR-CALUX. For identification of compounds exhibiting activity in the bioassays, either one or two-dimensional GC in combination with quadrupole (MSD), ion trap (ITD) or time-of-flight mass spectrometric detection (ToF-MS) was used, depending on the biological and chemical characteristics and the complexity of the fractions. The natural estrogenic hormone 17-β-estradiol and its metabolite estrone were identified with GC-ITD as the main contributors to the estrogenic activity. After successive rounds of fractionation, the dioxin-like activity could be explained by the presence of various polycyclic aromatic hydrocarbons identified with GC-MSD and two-dimensional comprehensive GC × GC-ToF-MS. Some estrogenic activity of a relatively non-polar nature remained unidentified. © 2006 Elsevier Ltd. All rights reserved.