diff --git a/django/contrib/admin/checks.py b/django/contrib/admin/checks.py
index c15216ddd86..5cb9d1e4627 100644
--- a/django/contrib/admin/checks.py
+++ b/django/contrib/admin/checks.py
@@ -11,12 +11,9 @@ from django.forms.models import BaseModelForm, _get_foreign_key, BaseModelFormSe
 
 
 def check_admin_app(**kwargs):
-    from django.contrib.admin.sites import site
+    from django.contrib.admin.sites import system_check_errors
 
-    return list(chain.from_iterable(
-        model_admin.check(model, **kwargs)
-        for model, model_admin in site._registry.items()
-    ))
+    return system_check_errors
 
 
 class BaseModelAdminChecks(object):
diff --git a/django/contrib/admin/sites.py b/django/contrib/admin/sites.py
index 3a69afda4a6..8b46a7e5460 100644
--- a/django/contrib/admin/sites.py
+++ b/django/contrib/admin/sites.py
@@ -15,6 +15,8 @@ from django.utils.translation import ugettext_lazy, ugettext as _
 from django.views.decorators.cache import never_cache
 from django.conf import settings
 
+system_check_errors = []
+
 
 class AlreadyRegistered(Exception):
     pass
@@ -99,7 +101,7 @@ class AdminSite(object):
                     admin_class = type("%sAdmin" % model.__name__, (admin_class,), options)
 
                 if admin_class is not ModelAdmin and settings.DEBUG:
-                    admin_class.check(model)
+                    system_check_errors.extend(admin_class.check(model))
 
                 # Instantiate the admin class to save in the registry
                 self._registry[model] = admin_class(model, self)
diff --git a/docs/releases/1.7.2.txt b/docs/releases/1.7.2.txt
index 860c8195256..88f3d3e1d88 100644
--- a/docs/releases/1.7.2.txt
+++ b/docs/releases/1.7.2.txt
@@ -149,3 +149,5 @@ Bugfixes
 
 * Restored the ``pre_migrate`` signal if all apps have migrations
   (:ticket:`23975`).
+
+* Made admin system checks run for custom ``AdminSite``\s (:ticket:`23497`).
diff --git a/tests/admin_checks/tests.py b/tests/admin_checks/tests.py
index 1e9b6f46461..500a889c71d 100644
--- a/tests/admin_checks/tests.py
+++ b/tests/admin_checks/tests.py
@@ -35,18 +35,20 @@ class ValidFormFieldsets(admin.ModelAdmin):
     )
 
 
+class MyAdmin(admin.ModelAdmin):
+    @classmethod
+    def check(cls, model, **kwargs):
+        return ['error!']
+
+
 @override_settings(
     SILENCED_SYSTEM_CHECKS=['fields.W342'],  # ForeignKey(unique=True)
     INSTALLED_APPS=['django.contrib.auth', 'django.contrib.contenttypes', 'admin_checks']
 )
 class SystemChecksTestCase(TestCase):
 
+    @override_settings(DEBUG=True)
     def test_checks_are_performed(self):
-        class MyAdmin(admin.ModelAdmin):
-            @classmethod
-            def check(self, model, **kwargs):
-                return ['error!']
-
         admin.site.register(Song, MyAdmin)
         try:
             errors = checks.run_checks()
@@ -54,6 +56,22 @@ class SystemChecksTestCase(TestCase):
             self.assertEqual(errors, expected)
         finally:
             admin.site.unregister(Song)
+            admin.sites.system_check_errors = []
+
+    @override_settings(DEBUG=True)
+    def test_custom_adminsite(self):
+        class CustomAdminSite(admin.AdminSite):
+            pass
+
+        custom_site = CustomAdminSite()
+        custom_site.register(Song, MyAdmin)
+        try:
+            errors = checks.run_checks()
+            expected = ['error!']
+            self.assertEqual(errors, expected)
+        finally:
+            custom_site.unregister(Song)
+            admin.sites.system_check_errors = []
 
     def test_readonly_and_editable(self):
         class SongAdmin(admin.ModelAdmin):