diff -Naur filterbynodetype/filterbynodetype.module filterbynodetype+comments/filterbynodetype.module
--- filterbynodetype/filterbynodetype.module	2008-10-23 07:29:33.000000000 +0200
+++ filterbynodetype+comments/filterbynodetype.module	2008-12-26 13:38:28.203125000 +0100
@@ -15,7 +15,9 @@
  * Implementation of hook_perm().
  */
 function filterbynodetype_perm() {
-  return array('bypass filter restrictions');
+  return array(
+    'administer filter restrictions',
+    'bypass filter restrictions');
 }
 
 /**
@@ -24,7 +26,7 @@
  * Allow users with the necessary permission to change what input formats
  * are allowed on a give node type.
  */
-function filterbynodetype_form_node_type_form_alter(&$form, $form_state) {
+function _filterbynodetype_form_node_type_form_alter(&$form, $form_state) {
 
   $options = array();
   foreach (filter_formats() as $format) {
@@ -45,6 +47,20 @@
     '#access' => user_access('adminster filters'),
   );
 
+  $comment_defaults = array();
+  foreach (filter_formats() as $format) {
+    $comment_defaults[] = variable_get('filterbynodetype_' . $format->format . '_' . $form['#node_type']->type . '_comment', 1);
+  }
+
+  $form['comment']['comment_input_formats'] = array(
+    '#type' => 'checkboxes',
+    '#title' => t('Allowed input formats'),
+    '#description' => t('Specify which input formats will be allowed on this node type\'s comments.  Note that a user must still have access to the appropriate input format in order to be able to use it.'),
+    '#options' => $options,
+    '#default_value' => $comment_defaults,
+    '#access' => user_access('adminster filters'),
+  );
+
   // Attach our submit handler so we can save our extra values.
   $form['#submit'][] = 'filterbynodetype_node_type_form_submit';
 }
@@ -58,6 +74,49 @@
   $form_values = $form_state['values'];
   foreach (filter_formats() as $format) {
     variable_set('filterbynodetype_' . $format->format . '_' . $form_values['type'], $form_values['input_formats'][$format->format]);
+    variable_set('filterbynodetype_' . $format->format . '_' . $form_values['type'] . '_comment', $form_values['comment_input_formats'][$format->format]);
+  }
+}
+
+function filterbynodetype_form_alter_format($type, &$container, $suffix) {
+
+  $formats =& $container['format'];
+
+  foreach (element_children($formats) as $element) {
+    if (isset($formats[$element]['#return_value']) && ! variable_get('filterbynodetype_' . $formats[$element]['#return_value'] . $suffix, 1)) {
+      unset($formats[$element]);
+    }
+  }
+
+  if (2 == count(element_children($formats))) { // 1 format and 1 extra item for the link
+    // If there's only one filter left, fold it down to just the description
+    $formats = $container['format'];
+    unset($container['format']);
+    // We don't know what the IDs are of the two fields, so we have to iterate to get them.
+    foreach (element_children($formats) as $element) {
+      if (isset($formats[$element]['#title'])) {
+        // This is a filter, so we assign it to the filter set as the only option.
+        $container['format'][$element] = array(
+          '#type' => 'value',
+          '#value' => $element,
+          '#parents' => array('format'),
+        );
+        $container['format']['format'] = array( // I have no idea why it uses this structure, but this is what filter.module does.
+          '#type' => 'item',
+          '#description' => $formats[$element]['#description'],
+        );
+      }
+      else {
+        // It's the guidelines text.
+        $container['format']['guidelines_link'] = array(
+          '#value' => $formats[$element]['#value'],
+        );
+      }
+    }
+  }
+  
+  if (1 == count(element_children($formats))) { // 1 extra item for the link, which means there's no filters left
+    // Do nothing.  The form becomes unsubmittable all on its own.
   }
 }
 
@@ -66,44 +125,22 @@
  */
 function filterbynodetype_form_alter(&$form, $form_state, $form_id) {
 
+  if ($form['#id'] == 'node-type-form' && user_access('administer filter restrictions')) {
+    _filterbynodetype_form_node_type_form_alter(&$form, $form_state);
+  }
+
   // For node edit forms, filter out disallowed input formats.
-  if (isset($form['#node']) && $form['#node']->type .'_node_form' == $form_id && !user_access('bypass filter restrictions')) {
+  if ($form['#id'] == 'node-form' && !user_access('bypass filter restrictions')) {
     $type = $form['type']['#value'];
-    $formats =& $form['body_field']['format'];
-    foreach (element_children($formats) as $element) {
-      if (isset($formats[$element]['#return_value']) && ! variable_get('filterbynodetype_' . $formats[$element]['#return_value'] . '_' . $type, 1)) {
-        unset($formats[$element]);
-      }
-    }
+    $container =& $form['body_field'];
+    filterbynodetype_form_alter_format($type, &$container, '_' . $type);
+  }
 
-    if (2 == count(element_children($formats))) { // 1 format and 1 extra item for the link
-      // If there's only one filter left, fold it down to just the description
-      $formats = $form['body_field']['format'];
-      unset($form['body_field']['format']);
-      // We don't know what the IDs are of the two fields, so we have to iterate to get them.
-      foreach (element_children($formats) as $element) {
-        if (isset($formats[$element]['#title'])) {
-          // This is a filter, so we assign it to the filter set as the only option.
-          $form['body_field']['format'][$element] = array(
-            '#type' => 'value',
-            '#value' => $element,
-            '#parents' => array('format'),
-          );
-          $form['body_field']['format']['format'] = array( // I have no idea why it uses this structure, but this is what filter.module does.
-            '#type' => 'item',
-            '#description' => $formats[$element]['#description'],
-          );
-        }
-        else {
-          // It's the guidelines text.
-          $form['body_field']['format']['guidelines_link'] = array(
-            '#value' => $formats[$element]['#value'],
-          );
-        }
-      }
-    }
-    if (1 == count(element_children($formats))) { // 1 extra item for the link, which means there's no filters left
-      // Do nothing.  The form becomes unsubmittable all on its own.
-    }
+  // For comment edit forms, filter out disallowed input formats.
+  if ($form['#id'] == 'comment-form' && !user_access('bypass filter restrictions')) {
+    $type = node_load($form['nid']['#value'])->type;
+
+    $container =& $form['comment_filter'];
+    filterbynodetype_form_alter_format($type, &$container, '_' . $type . '_comment');
   }
 }