OBJECTIVE To determine the sensitivity and specificity of surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF-MS) assay for head and neck squamous cell carcinoma (HNSCC) disease surveillance. METHODS The SELDI-TOF-MS serum protein profiles of patients with HNSCC were analyzed to determine the sensitivity and specificity of the SELDI assay for HNSCC detection following definitive treatment. METHODS Academic research. METHODS Thirty-two patients with previously untreated HNSCC. METHODS Serum samples were collected prospectively at 3-month intervals following treatment during a 24-month follow-up period. METHODS Ninety-three serum samples were analyzed. RESULTS The SELDI-TOF-MS identified protein peaks in the range of 0 to 100 kDa. Classification tree analysis based on peak expression distinguished pretreatment from 6-month posttreatment samples with 75.0% sensitivity and 87.5% specificity. Samples collected at 3 months following treatment did not significantly differ from pretreatment samples. Serum samples from patients who were disease free at 6 months or longer following treatment differed from matched pretreatment samples by the overexpression of a protein peak at 6495 Da, while serum samples from patients with recurrence differed from matched pretreatment samples by the underexpression of a protein peak at 4493 Da. CONCLUSIONS Proteomic analysis of serum protein profiles distinguishes pretreatment and posttreatment samples from patients with HNSCC with a high degree of sensitivity and specificity. After 6 months, serum protein profiles seem to have distinct differences in peak expression based on disease status. Further investigation of the clinical usefulness of this technology in HNSCC detection and surveillance is warranted.