return theme('item_list', array('header' => $header,'items' => $rows));

/**
 * Implements hook_theme().
 */
function MYMODULE_theme($existing, $type, $theme, $path) {
  $custom_theme = array();
  $custom_theme['my_new_theme'] = array(
    // example theme template register
    // for
    //sites/all/modules/mymodule/templates/my_new_theme.tpl.php
    'template' => 'my-new-theme',//dash will convert to underscore in template name.
    'path' => drupal_get_path('module', 'mymodule') . '/templates',
    'variables' => array('header' => null,'rows'=>null),
  );

  return $custom_theme;
}

theme('my_new_theme', array('header' => $header, 'rows' => $rows));