diff --git a/includes/form.inc b/includes/form.inc
index f41cce4a735..9b67da8a3f9 100644
--- a/includes/form.inc
+++ b/includes/form.inc
@@ -1978,8 +1978,22 @@ function form_type_checkboxes_value($element, $input = FALSE) {
     }
     return $value;
   }
+  elseif (is_array($input)) {
+    // Programmatic form submissions use NULL to indicate that a checkbox
+    // should be unchecked; see drupal_form_submit(). We therefore remove all
+    // NULL elements from the array before constructing the return value, to
+    // simulate the behavior of web browsers (which do not send unchecked
+    // checkboxes to the server at all). This will not affect non-programmatic
+    // form submissions, since a checkbox can never legitimately be NULL.
+    foreach ($input as $key => $value) {
+      if (is_null($value)) {
+        unset($input[$key]);
+      }
+    }
+    return drupal_map_assoc($input);
+  }
   else {
-    return is_array($input) ? drupal_map_assoc($input) : array();
+    return array();
   }
 }
 
diff --git a/modules/simpletest/tests/form.test b/modules/simpletest/tests/form.test
index d139f4dcb7d..2e1564a6ea3 100644
--- a/modules/simpletest/tests/form.test
+++ b/modules/simpletest/tests/form.test
@@ -973,10 +973,19 @@ class FormsProgrammaticTestCase extends DrupalWebTestCase {
     $current_batch = $batch =& batch_get();
     $batch = array();
 
-    $this->submitForm();
-    $this->submitForm('test 1');
-    $this->submitForm();
-    $this->submitForm('test 2');
+    // Test that a programmatic form submission is rejected when a required
+    // textfield is omitted and correctly processed when it is provided.
+    $this->submitForm(array(), FALSE);
+    $this->submitForm(array('textfield' => 'test 1'), TRUE);
+    $this->submitForm(array(), FALSE);
+    $this->submitForm(array('textfield' => 'test 2'), TRUE);
+
+    // Test that a programmatic form submission can turn on and off checkboxes
+    // which are, by default, checked.
+    $this->submitForm(array('textfield' => 'dummy value', 'checkboxes' => array(1 => 1, 2 => 2)), TRUE);
+    $this->submitForm(array('textfield' => 'dummy value', 'checkboxes' => array(1 => 1, 2 => NULL)), TRUE);
+    $this->submitForm(array('textfield' => 'dummy value', 'checkboxes' => array(1 => NULL, 2 => 2)), TRUE);
+    $this->submitForm(array('textfield' => 'dummy value', 'checkboxes' => array(1 => NULL, 2 => NULL)), TRUE);
 
     // Restore the current batch status.
     $batch = $current_batch;
@@ -984,30 +993,36 @@ class FormsProgrammaticTestCase extends DrupalWebTestCase {
 
   /**
    * Helper function used to programmatically submit the form defined in
-   * form_test.module with the given value.
+   * form_test.module with the given values.
    *
-   * @param string $value
-   *   The field value to be submitted.
+   * @param $values
+   *   An array of field values to be submitted.
+   * @param $valid_input
+   *   A boolean indicating whether or not the form submission is expected to
+   *   be valid.
    */
-  private function submitForm($value = NULL) {
-    // Programmatically submit the given value.
-    $form_state = array('values' => array('submitted_field' => $value));
+  private function submitForm($values, $valid_input) {
+    // Programmatically submit the given values.
+    $form_state = array('values' => $values);
     drupal_form_submit('form_test_programmatic_form', $form_state);
 
+    // Check that the form returns an error when expected, and vice versa.
     $errors = form_get_errors();
     $valid_form = empty($errors);
-    $valid_input = !empty($value);
-
-    // If no value was passed the form should return an error and viceversa.
-    $args = array('%value' => $value, '%errors' => $valid_form ? '' : implode(' ', $errors));
-    $this->assertTrue($valid_input == $valid_form, t('Input value: %value<br/>Validation handler errors: %errors', $args));
+    $args = array(
+      '%values' => print_r($values, TRUE),
+      '%errors' => $valid_form ? t('None') : implode(' ', $errors),
+    );
+    $this->assertTrue($valid_input == $valid_form, t('Input values: %values<br/>Validation handler errors: %errors', $args));
 
     // We check submitted values only if we have a valid input.
     if ($valid_input) {
-      // By fetching the value from $form_state['storage'] we ensure that the
+      // By fetching the values from $form_state['storage'] we ensure that the
       // submission handler was properly executed.
-      $submitted_value = $form_state['storage']['programmatic_form_submit'];
-      $this->assertTrue($submitted_value == $value, t('Submission handler correctly executed: %submitted_value', array('%submitted_value' => $submitted_value)));
+      $stored_values = $form_state['storage']['programmatic_form_submit'];
+      foreach ($values as $key => $value) {
+        $this->assertTrue(isset($stored_values[$key]) && $stored_values[$key] == $value, t('Submission handler correctly executed: %stored_key is %stored_value', array('%stored_key' => $key, '%stored_value' => print_r($value, TRUE))));
+      }
     }
   }
 }
diff --git a/modules/simpletest/tests/form_test.module b/modules/simpletest/tests/form_test.module
index 6eb209fa536..2fb4937dec3 100644
--- a/modules/simpletest/tests/form_test.module
+++ b/modules/simpletest/tests/form_test.module
@@ -1051,10 +1051,20 @@ function form_test_form_form_test_state_persist_alter(&$form, &$form_state) {
  * Form builder to test programmatic form submissions.
  */
 function form_test_programmatic_form($form, &$form_state) {
-  $form['submitted_field'] = array(
-    '#title' => 'Submitted',
+  $form['textfield'] = array(
+    '#title' => 'Textfield',
     '#type' => 'textfield',
   );
+  $form['checkboxes'] = array(
+    '#type' => 'checkboxes',
+    '#options' => array(
+      1 => 'First checkbox',
+      2 => 'Second checkbox',
+    ),
+    // Both checkboxes are selected by default so that we can test the ability
+    // of programmatic form submissions to uncheck them.
+    '#default_value' => array(1, 2),
+  );
 
   return $form;
 }
@@ -1066,8 +1076,8 @@ function form_test_programmatic_form($form, &$form_state) {
  * explicitly required here.
  */
 function form_test_programmatic_form_validate($form, &$form_state) {
-  if (empty($form_state['values']['submitted_field'])) {
-    form_set_error('submitted_field', t('Submitted field is required.'));
+  if (empty($form_state['values']['textfield'])) {
+    form_set_error('textfield', t('Textfield is required.'));
   }
 }
 
@@ -1075,10 +1085,10 @@ function form_test_programmatic_form_validate($form, &$form_state) {
  * Form submit handler for programmatic form submissions.
  *
  * To test that the submission handler is correctly executed, we store the
- * submitted value in a place we can access from the caller context.
+ * submitted values in a place we can access from the caller context.
  */
 function form_test_programmatic_form_submit($form, &$form_state) {
-  $form_state['storage']['programmatic_form_submit'] = $form_state['values']['submitted_field'];
+  $form_state['storage']['programmatic_form_submit'] = $form_state['values'];
 }
 
 /**