We analysed urine cell-free DNA samples from two cohorts using an amplicon-sequencing MSI assay: (1) Sequential cases of upper tract urothelial carcinoma (UTUC) provided paired tumour/pre-operative urine samples for MSI analysis and mismatch repair protein immunohistochemistry (MMR IHC) and those with an MMR deficient (MMRd) tumour were offered constitutional Lynch syndrome testing (2) Eligible individuals with a diagnosis of MSH2-Lynch syndrome (aged 30–75 years, without recent cancer diagnosis) were offered urine MSI analysis via a clinic appointment or postal urine sample collection. Here, MRC1 is linked to renal pelvis/ureter urothelial carcinoma.