Measurements of the prostaglandin (PGD2) metabolite 9 alpha, 11 beta-PGF2 in unextracted urine performed by enzyme immunoassay (EIA) were compared with values obtained by negative chemical ionisation gas chromatography-mass spectrometry (NCI GC-MS). Values determined by NCI GC-MS were in the same range but consistently lower than those obtained by EIA, suggesting that other endogenous compounds could be contributing to the immunoreactivity. Isoprostanes were generated by autoxidation of arachidonic acid and the 9 alpha, 11 beta-PGF2 antibody demonstrated less than 0.7% crossreactivity to the mix, making it unlikely that isoprostanes in urine interfere with quantification of 9 alpha, 11 beta-PGF2 by EIA. This was further supported by the 70% reduction in immunoreactive material measured in urine after three days treatment in a healthy volunteer with the cyclooxygenase inhibitor ibuprofen. Purification of urine samples by reverse phase high-performance liquid chromatography (HPLC) revealed the presence of two immunoreactive compounds in addition to 9 alpha, 11 beta-PGF2. The compounds were identified as dinor compounds by NCI GC-MS. One of the compounds was identical to 9 alpha, 11 beta-2,3-dinor-PGF2 which was generated by beta-oxidation of 9 alpha, 11 beta-PGF2 and identified by electron impact (EI)-GC-MS. In conclusion, urinary 9 alpha, 11 beta-PGF2 concentrations measured by EIA represent the sum of 9 alpha, 11 beta-PGF2 and two isomers of its dinor metabolite. Thus, the direct EIA is fast, sensitive and sufficiently specific to monitor activation of the PGD2 pathway, thereby providing a valuable clinical tool to assess the status of mast cell activation in vivo.