This study aimed to compare the sensitivity and accuracy of two methods of quantitative real-time polymerase chain reaction (qrt-PCR), in order to determine haematopoietic chimerism (CH): single nucleotide polymorphisms using TaqMan (TM) probes and insertion/deletion polymorphisms using Hybridization (Hyb) probes. A total of 106 samples from 20 patients who underwent allogenic stem cell transplantation (n = 14) or live-donor liver transplantation (n = 6) were studied. The mean level of chimerism was 8.37% for the TM method and 7.73% in the Hyb method, which was not significantly different (P = 0.69). The Pearson correlation coefficient between the two methods was r = 0.91 (P < 0.001). The estimation of the regression line, using the Passing and Balbock method was Intercept A -0.0381 [95% confidence interval (CI) -0.1265 to 0.0296) and Slope B: 1.04609(95% CI 0.9349-1.161). Bland-Altman data showed that the standard deviations, which differed between the two methods (%Hyb-%TM), were 0.98 and -1.28. The accuracy and sensitivity of qrt-PCR chimerism is independent of the method used if the optimization is adequate and satisfies the criteria for adequate study. Real-time PCR, independent of the method adopted, is a very good tool for study levels of CH.