Olive mill waste water (OMWW) is a major environmental issue in the Mediterranean. We address this problem by investigating the wastes for the presence of biologically active compounds already detected in both olive oil and pomace. Two initial OMWW samples were filtered using two microporous filtering media: (a) clayey diatomite and (b) zeolitic volcanic tuffs, obtaining three filtered samples from each. All initial and filtrated samples were tested for their activity on platelet activating factor (PAF)-induced aggregation. The results showed that the initial samples contain biologically active compounds (PAF inhibitors) and that in their respective last-eluted filtered samples these compounds are purified. These eluted samples, along with their corresponding initial OMWW, were further separated with HPLC and the purified fractions responsible for the aforementioned biological activity, were further studied using chemical determinations and MS analysis. It was confirmed that the PAF inhibitor present in these fractions resembles the one isolated from olive oil. These results offer a new approach on the OMWW handling by offering an alternative use of this waste as starting material for nutritional and/or pharmaceutical purposes in the future.