A cation exchange resin was used to extract water soluble EPS material from different sewer biofilms and a biofilm monoculture of P.putida. The extraction method seemed to be especially suitable for extracting humic substances and proteins from biofilms but also carbohydrate could be extracted, depending on the nature of the sample. Extraction conditions must be well defined because the extraction efficiency was dependent on stirring intensity, amount of cation exchange resin and extraction time. Up to 20% of the total biofilm protein was found in the DOWEX-extractable fraction. No significant cell-lysis up to 2 hours of extraction time could be detected by acridine orange (AO) direct counts. The same was true when applying the extraction method to a batch culture of P.putida. However, the number of viable cells in the batch culture as recorded by plate count technique was reduced to 28 % after 30 min of extraction. In conclusion, proteins and humic substances can be extracted from biofilm EPS in considerable amounts and should be investigated more in detail when analysing the properties of the EPS matrix of a biofilm.