Abstract: Purpose Circulating tumour DNA (ctDNA) analysis has demonstrated utility for diagnostic and prognostic applications in many cancer types, including metastatic prostate cancer. However, localised prostate cancer yields relatively low levels of ctDNA and therefore it has been difficult to detect in this context using conventional methods. We aimed to assess the limits of detection of ctDNA in localised prostate cancer by leveraging thousands of patient-specific mutations per case with the high-sensitivity INVAR method, and to test the hypothesis that ctDNA detection is associated with high risk disease. Experimental Procedures A total of 128 individuals with clinically localised prostate cancer at the time of sample collection were selected from cohorts in Australia (n=48) and the UK (n=80). Additionally, 27 healthy individuals without prostate cancer were included as negative controls. Primary tumour tissue and matched bloods from all cases were whole genome sequenced (WGS) and somatic variants were called using pipelines from the Pan Prostate Cancer Group. Plasma cell-free DNA (cfDNA) samples from cases and controls were profiled using custom targeted sequencing panels, with saturating coverage of patient-specific mutations identified by WGS. We assessed ctDNA detection in cases using the highly sensitive INVAR pipeline, that leverages consensus read sequencing alignments, background error modelling and integration of signals across thousands of patient-specific variants. Biochemical recurrence and metastasis-free survival curves were used to assess the relationship between ctDNA detection and disease progression. Results We analysed pre-treatment blood plasma ctDNA in a large cohort of localised prostate cancer patients, using error-suppressed targeted sequencing of over 280k patient-specific mutations. To comprehensively assess ctDNA mutation analysis in this context, we combined signals across the maximum number of genome-wide patient specific mutations and leveraged an established analysis pipeline (INVAR) that corrects for background error rates and calculates a global integrated mutant allele fraction. ctDNA was detected in 9.3% of localised prostate cancer patients. In cases where ctDNA was detected we found significant associations with biochemical recurrence (p=0.01) and shorter metastasis-free survival (p {$<$} 0.0001). Conclusions Our study provides clear insights into the required analytical sensitivity and potential utility of ctDNA mutation analysis in localised prostate cancer. We found that mutation-based ctDNA detection rates were low in localised prostate cancer ({$<$}10% cases), but in ctDNA positive cases there was a significant association with relapse after surgical intervention alone. This raises the potential for including ctDNA detection as an additional tool for patient stratification in future neo/adjuvant treatment trials aiming to assess the impact of treatment escalation in men at high risk of relapse with current standard of care treatment alone.