Next-generation sequencing (NGS) has improved the sensitivity of chimerism assays beyond the limitations of conventional short tandem repeat (STR) methods, enabling the detection of minimal recipient haematopoiesis after haematopoietic stem cell transplantation (HSCT). We evaluated the clinical utility of CASAL, an NGS-based chimerism assay, in routine practice. We retrospectively analysed 310 patients who underwent STR or CASAL chimerism testing between April 2021 and September 2023. CASAL provided significantly more informative markers than STR (median 18 vs. 6; p < 0.001). Among 260 CASAL samples with paired molecular minimal residual disease (MRD) data, concordance at the 10(-4) threshold was ~84%. Low-level mixed chimerism (2%-5%) detected beyond 1 month post-HSCT was associated with impending relapse. In survival analyses, patients with both MC and MRD positivity (MC/MRD(+)) had the highest relapse risk across both platforms. Multivariable Cox regression confirmed MC/MRD(+) as an independent predictor of relapse (hazard ratio 5.87, 95% CI: 1.17-29.57). CASAL enables sensitive chimerism monitoring and shows a strong correlation with molecular MRD and clinical outcomes. These findings support its clinical utility for individualized post-HSCT surveillance, especially in patients lacking leukaemia-specific molecular targets.