Background Torquetenovirus (TTV) viremia is emerging as a promising tool to assess functional immune competence, to predict posttransplant immune‐related complications, and eventually to customize immunosuppression. Methods In this study, 327 blood samples were tested using two real‐time PCR (rtPCR) assays both targeted to the untranslated region of the TTV genome. The first assay was an in‐house rtPCR developed by our group, the second one was the recently marketed TTV R‐GENE assay. Results In the validation study, the TTV R‐GENE showed good performances in precision and reproducibility, and sensitivity as low as 12 TTV DNA copies/mL, like previously reported for the in‐house rtPCR. The Bland‐Altman analysis showed that the mean difference between the two methods was −0.3 log copies/mL. In the comparison study, 69% and 72% of samples were detected positive by rtPCR and TTV R‐GENE, respectively (94% concordance, κ = 0.88). Performances did not differ between the two rtPCRs by type of TTV group examined. When a newly‐developed in‐house digital droplet PCR was applied for TTV quantification and used as an alternative method of comparison on 94 samples, the results strongly correlated with those obtained by the two rtPCR methods (99% concordance). Conclusion In summary, all the molecular methods assayed are highly sensitive and accurate in quantitation of TTV DNA in blood samples. Highlight TTV monitoring is a promising strategy for quantification of the immunocompetence in transplant patients. PCR methods actually in use have comparable performances in TTV quantification