Inconsistency in prognostic scores occurs where two different risk categories are applied to the same chronic myeloid leukemia (CML) patient. This study evaluated common scoring systems for identifying risk groups based on patients' molecular responses to select the best prognostic score when conflict prognoses are obtained from patient profiles. We analyzed 104 patients diagnosed with CML and treated at King Abdulaziz Medical City, Saudi Arabia, who were monitored for major molecular response (achieving a BCR-ABL1 transcript level equal to or less than 0.1%) by Real-Time Quantitative Polymerase Chain Reaction (RQ-PCR), and their risk profiles were identified using Sokal, Hasford, EUTOS, and ELTS scores based on the patients' clinical and hematological parameters at diagnosis. Our results found that the Hasford score outperformed other scores in identifying risk categories for conflict groups, with an accuracy of 63%.