This study determined isomeric molecules by employing molecular imprinting technology (MIP) and electrochemical impedance spectroscopy (EIS). In order to increase surface area to obtain more sensitive sensor technology, ex situ precipitation polymerization was carried out to produce microspheres. These microspheres were placed on pyrrole-modified carbon electrodes. Acrylamide, as monomer, was polymerized by cross-linker trimethylolpropane trimethacrylate (TRIM) and Azobisisobutyronitrile (AIBN) as initiator and as template molecules; chondroitin sulfate (CS) and dermatane sulfate (DS) were used. Performances of the electrodes were determined as follows, CS and DS sensor, respectively; calibration curves were calculated between 50 to 500 ng/mL and 50 to 600 ng, R-2 = 0.9942 +/- 0.0029 and R-2 = 0.9824 +/- 0.0083, LOD and LOQ were 15.19 ng/mL, 46.03 ng/mL, and 32.56 ng/mL, 102.82 ng/mL, respectively. The characterization of polymers was carried out by X-ray photoelectron spectroscopy (XPS), Fourier Transform Infrared (FTIR), and Scanning Electron Microscopy (SEM). The applicability of the optimized sensor systems to real samples was examined in urine samples and the systems were tested by LC-MS/MS method. Sensors showed a good correlation with tandem mass spectrometry.