In this study, a short amplicon (53 bp) qPCR assay targeting HCC-associated hotspot CTNNB1 exon 3 mutations in codon 32–37 was used for mutation detection in urine cfDNA from patients with HCC and to investigate the feasibility of using urine DNA markers as a prognostic marker for HCC recurrence and for detecting minimum residual disease after treatment. Here, CTNNB1 is linked to hepatocellular carcinoma.