We report an improved LC-MS-MS assay that accurately measures prostaglandins D 2 (PGD 2 ) and E 2 (PGE 2 ) in cell culture supernatants and other biological fluids. The limit of detection for each prostaglandin was 20 pg/mL (0.20 pg; 0.55 fmol on-column), and the inter-day and intra-day coefficients of variation were less than 5%. Both d 4 -PGE 2 and d 4 -PGD 2 were used as surrogate standards to control for differential loss and degradation of the analytes. Stability studies indicated that sample preparation time should be less than 8 h to measure PGD 2 accurately, whereas preparation time did not affect PGE 2 measurement due to its greater stability in biological samples. As an application of the method, PGD 2 and PGE 2 were measured in culture supernatants from A549 cells and RAW 264.7 cells. The human lung alveolar cell line A549 was found to produce PGE 2 but no PGD 2 while the murine macrophage cell line RAW 264.7 produced PGD 2 and only trace amounts of PGE 2 . This direct comparison showed that COX-2 gene expression can lead to differential production of PGD 2 and PGE 2 by epithelial cells and macrophages. Since PGE 2 is anti-asthmatic and PGD 2 is pro-asthmatic, we speculate that the balance of production of these eicosanoids by epithelial cells and macropahges in the lung contributes to the pathogenesis of COPD, bronchiectasis, asthma, and lung cancer.