Index: src/wp-admin/includes/schema.php
===================================================================
--- src/wp-admin/includes/schema.php	(revision 33801)
+++ src/wp-admin/includes/schema.php	(working copy)
@@ -507,6 +507,9 @@
 			? $wp_current_db_version : $wp_db_version;
 	}
 
+	// x.y.z
+	$options[ 'theme_mods_' . $options['stylesheet'] ] = array();
+
 	// 3.0 multisite
 	if ( is_multisite() ) {
 		/* translators: blog tagline */
Index: tests/phpunit/tests/theme.php
===================================================================
--- tests/phpunit/tests/theme.php	(revision 33801)
+++ tests/phpunit/tests/theme.php	(working copy)
@@ -296,4 +296,14 @@
 		$this->assertEquals($template, get_template());
 		$this->assertEquals($style, get_stylesheet());
 	}
+
+	/**
+	 * Test that installation added a "theme_mods_" option for the default theme.
+	 */
+	function test_populate_options_theme_mod() {
+		$stylesheet = get_option( 'stylesheet' );
+		$this->assertSame( WP_DEFAULT_THEME, $stylesheet );
+		$this->assertSame( array(), get_option( "theme_mods_{$stylesheet}" ) );
+	}
+
 }