The aim of this project was to investigate molecular imprinted polymers (MIPs) for their potential use in a two-dimensional (2D) capillary liquid chromatography (cLC) system for the simultaneous determination of prostaglandins (PGs) in human mesenchymal stem cells (hMSCs) supernatant. The polymers using arachidonic acid (AA) as MIP template were prepared as packing material by crushing, sieving and sedimentation. Both slurry-packing and dry-packing methods were investigated to pack miniaturized columns. The slurry-packing of a fused silica column (0.32 mm inner diameter (I.D.) × 35 mm) failed due to high back pressure, while steel columns (0.7 mm I.D. × 35 mm) which were dry-packed could be used for testing possible imprinting effects.Columns dry-packed with a MIP and its corresponding non-imprinted polymer (NIP) were tested, respectively. The tests were carried out at both normal phase (NP) and reversed phase (RP) conditions with different mobile phase (MP) compositions. Both prostaglandin A1 (PGA1) and the template AA were used for testing the columns. Detection was carried out by mass spectrometry (MS). The testing showed that MIP IL-22 (M-22) had possible imprinting effect for both PGA1 and AA, while MIP IL-25 (M-25) and MIP IL-32 (M-32) had possible imprinting effect for AA. MIP IL-30 (M-30) and MIP IL-31 (M-31) did not show imprinting effect for AA at neither NP nor RP conditions.