Benchmark the Drupal bootstrap phases. Since this is something that happens on every page load it needs to be really fast. You should probably be worried if bootstrap is taking more than 300ms per page load.

benchmark-drupal-bootstrap.php

<?php
define('DRUPAL_ROOT', getcwd());


require_once DRUPAL_ROOT . '/includes/bootstrap.inc';

$phases = array(
  'CONFIGURATION' => DRUPAL_BOOTSTRAP_CONFIGURATION,
  'PAGE_CACHE' => DRUPAL_BOOTSTRAP_PAGE_CACHE,
  'DATABASE' => DRUPAL_BOOTSTRAP_DATABASE,
  'VARIABLES' => DRUPAL_BOOTSTRAP_VARIABLES,
  'SESSION' => DRUPAL_BOOTSTRAP_SESSION,
  'PAGE_HEADER' => DRUPAL_BOOTSTRAP_PAGE_HEADER,
  'LANGUAGE' => DRUPAL_BOOTSTRAP_LANGUAGE,
  'FULL' => DRUPAL_BOOTSTRAP_FULL,
);

timer_start('complete_run');
foreach ($phases as $id => $phase) {
  timer_start('bootstrap_' . $id);
  drupal_bootstrap($phase);
  $t = timer_stop('bootstrap_' . $id);
  echo $id . ': ' . $t['time'] . '<br />';
}
$t = timer_stop('complete_run');
echo "<br />TOTAL: " . $t['time'];