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Liquid biopsy markers of minimal residual disease (MRD) after cancer treatment have been investigated for detection of recurrence, but detection of locoregional MRD using plasma remains a challenge. Our laboratory examined the use of liquid biopsy technology in surgical drain fluid (SDF) immediately after surgery. Here, we: 1) validate the detection of tumor-associated cell-free DNA (cfDNA) in SDF and 2) demonstrate the utility of SDF cfDNA for clinical decision-making in two cancer types. We hypothesize that tumor-associated cfDNA in SDF provides an early, objective measure of locoregional MRD that can guide adjuvant therapy. We collected tumor, SDF, and plasma samples from patients undergoing surgery for HPV(+) oropharyngeal squamous cell carcinoma (OPSCC) and thyroid cancer. TaqMan qPCR assays were designed for detection of HPV DNA and BRAF V600 mutations in HPV (+) OPSCC and thyroid cancer, respectively. HPV(+) OPSCC PCR results were validated using next-generation HPV capture sequencing in a subset of patients. 62 HPV (+) OPSCC and 13 thyroid carcinoma cases were included. We correlated SDF HPV cfDNA with pathology and showed a dose-dependence between HPV copy number, node positivity, and extranodal extension (ENE). In patients with ENE, locoregional MRD detection rate was 93% in SDF versus 53% in plasma (p=0.035, Fisher's). We validated results using HPV capture sequencing in a subset (n=6) and noted 100% concordance between PCR data and HPV subtyping in SDF. We then measured actionable mutations in SDF and associations with locoregional recurrence. We determined BRAF V600 mutant status in 13 papillary and anaplastic thyroid carcinomas and in paired cfDNA from SDF. In three known BRAF V600 cases, two patients with extrathyroidal extension were SDF mutant positive; one recurred locoregionally while the other only recently had surgery. The SDF mutant negative patient is disease-free at 9 months. We present the use of a novel multi-omic platform to quantify tumor-associated cfDNA in surgical drain fluid as an immediate postoperative marker of locoregional MRD. Our data suggest tumor-associated cfDNA in surgical drain fluid is highly correlated with aggressive pathologic features in two cancer types, and could enable more accurate determination of adjuvant therapy and prognosis. When combined with plasma tumor-associated cfDNA, this may enable locoregional and distant molecular restaging after surgery. Future clinical applications may include identifying candidates for adjuvant therapy de-escalation after surgery in HPV+ OPSCC; in thyroid cancer, this assay could assist in radioactive iodine therapy planning or introduce targeted therapies into the adjuvant setting. [ABSTRACT FROM AUTHOR]