Histological affected or close margin is an adverse factor in conventional surgery of larynx-hypopharynx cancer. Our objective was to analyze the relevance of the margins in transoral laser microsurgery (TLM). A retrospective study of 357 consecutive patients with cancer of the larynx and hypopharynx (T1-T4) treated with TLM. Three possible margins were considered: tumor free, affected, and uncertain. An affected margin showed marked tumor infiltration. An uncertain margin was defined when the sample was insufficient, when it showed carbonization impeding accurate evaluation, or when tumor cells were less than 2 mm. Margins were free in 254 (71.1%) patients, affected in 64 (17.9%) and uncertain in 39 (10.9%). One hundred and three patients (28.9%) presented tumor relapse. The margins were associated with tumor relapse (P < 0.001), but were not significantly related to the tumor site (P = 0.307), the pT classification (P = 0.183), or the difficulty of surgical exposure (P = 0.427). Distant metastases were found in 4.7% of the patients with free margins, in 7.7% of those with uncertain margins, and in 14.1% with affected margins. These differences were statistically significant (P = 0.028). Tumor involvement of the surgical margin was associated with higher rates of local relapse, distant metastasis and the necessity of salvage surgery, together with a lower specific actuarial survival rate.