BACKGROUND: Colorectal cancer (CRC) remains a significant global health challenge, characterized by high morbidity and mortality rates. This study explores the potential of Alu-based cell-free DNA (cfDNA) and specific PIWI-interacting RNAs (piRNAs) as innovative biomarkers for monitoring treatment responses in CRC patients. METHODS: We analyzed plasma samples from 70 CRC patients, equally divided between those undergoing chemotherapy and surgical interventions. RESULTS: Our findings reveal that certain piRNAs, particularly piRNA-823, piRNA-54265, and piRNA-1245, exhibit significant prognostic value, with notable expression changes observed in the chemotherapy group compared to the surgery group. Furthermore, the levels of ALU-based cfDNA fragments showed a marked decrease post-chemotherapy, suggesting their utility in assessing therapeutic efficacy. CONCLUSIONS: This research underscores the importance of integrating these molecular tools particularly piRNA-823 and ALU-based cfDNA into clinical practice, potentially enhancing the management strategies for CRC patients and improving their outcomes.