There are several commonly used diagnostic methods to detect pestiviruses for routine diagnostic purposes. In the present study, we aimed to compare virus isolation-indirect immunoperoxidase monolayer assay (VI-IIPMA), antigen capture ELISA (ACE), and RT-PCR for the detection of pestiviruses in clinical samples. Out of 246 samples tested (11 serum, 119 swab, 116 tissue), 28 samples (11.39%) were positive and 218 (88.61%) were negative using the VI-IIPMA method. Using ACE, 70 samples (28.46%) were positive and 176 (71.54%) were negative. Finally, using RT-PCR analysis, we detected 19 (7.72%) positive and 227 (92.28%) negative samples. Inconsistencies were observed among results of the three methods: 8 samples were positive using VI-IIPMA but negative using ACE and RT-PCR. In addition, 4 samples that were found to be negative by VI-IIPMA were found to be positive by ACE and RT-PCR. Five samples were positive by ACE and VI-IIPMA. However, 46 samples were found to be positive only by ACE. These results show that the number of positive results detected by ACE is higher than that by VI-IIPMA and RT-PCR. Although ACE may prove advantageous for diagnosing pestiviruses, using a second method in combination with ACE will improve the validity of the results.