HTML:

<table id="mytable">
  <thead>
    <tr>
      <th>Header</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td>...</td>
    </tr>
  </tbody>
</table>

JavaScript:

document.getElementById("mytable").tBodies[0].innerHTML = '';

Or loop over tBodies, if you have more than one.