Background: Disease surveillance in patients with bladder cancer is important for early diagnosis of progression and metastasis and for optimised treatment. Objective: To develop urine and plasma assays for disease surveillance for patients with FGFR3 and PIK3CA tumour mutations. Design, setting, and participants: Droplet digital polymerase chain reaction (ddPCR) assays were developed and tumour DNA from two patient cohorts was screened for FGFR3 and PIK3CA hotspot mutations. One cohort included 363 patients with non-muscle-invasive bladder cancer (NMIBC). The other cohort included 468 patients with bladder cancer undergoing radical cystectomy (Cx). Urine supernatants (NMIBC n = 216, Cx n = 27) and plasma samples (NMIBC n = 39, Cx n = 27) from patients harbouring mutations were subsequently screened using ddPCR assays. Outcome measurements and statistical analysis: Progression-free survival, recurrence-free survival, and overall survival were measured. Fisher's exact test, the Wilcoxon rank-sum test and Cox regression analysis were applied. Results and limitations: In total, 36% of the NMIBC patients (129/363) and 11% of the Cx patients (44/403) harboured at least one FGFR3 or PIK3CA mutation. Screening of DNA from serial urine supernatants from the NMIBC cohort revealed that high levels of tumour DNA (tDNA) were associated with later disease progression in NMIBC (p = 0.003). Furthermore, high levels of tDNA in plasma samples were associated with recurrence in the Cx cohort (p = 0.016). A positive correlation between tDNA levels in urine and plasma was observed (correlation coefficient 0.6). The retrospective study design and low volumes of plasma available for analysis were limitations of the study. Conclusions: Increased levels of FGFR3 and PIK3CA mutated DNA in urine and plasma are indicative of later progression and metastasis in bladder cancer. Patient summary: Urine and plasma from patients with bladder cancer may be monitored for diagnosis of progression and metastasis using mutation assays. (C) 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.