diff --git a/src/CodeCoverage.php b/src/CodeCoverage.php
index 88326f0b7..e6127da52 100644
--- a/src/CodeCoverage.php
+++ b/src/CodeCoverage.php
@@ -54,6 +54,8 @@ class PHP_CodeCoverage
 
     /**
      * @var bool
+     *
+     * @deprecated
      */
     private $processUncoveredFilesFromWhitelist = false;
 
@@ -86,6 +88,13 @@ class PHP_CodeCoverage
      */
     private $tests = array();
 
+    /**
+     * Store all uncovered files
+     *
+     * @var array
+     */
+    private $uncoveredFiles = array();
+
     /**
      * Constructor.
      *
@@ -105,6 +114,8 @@ public function __construct(PHP_CodeCoverage_Driver $driver = null, PHP_CodeCove
 
         $this->driver = $driver;
         $this->filter = $filter;
+
+        $this->initData();
     }
 
     /**
@@ -219,7 +230,7 @@ public function start($id, $clear = false)
 
         $this->currentId = $id;
 
-        $this->driver->start();
+        $this->driver->start(false);
     }
 
     /**
@@ -250,6 +261,12 @@ public function stop($append = true, $linesToBeCovered = array(), array $linesTo
         $data = $this->driver->stop();
         $this->append($data, null, $append, $linesToBeCovered, $linesToBeUsed);
 
+        foreach (array_keys($data) as $file) {
+            if (isset($this->uncoveredFiles[$file])) {
+                unset($this->uncoveredFiles[$file]);
+            }
+        }
+
         $this->currentId = null;
 
         return $data;
@@ -576,7 +593,7 @@ private function applyIgnoredLinesFilter(array &$data)
     private function initializeFilesThatAreSeenTheFirstTime(array $data)
     {
         foreach ($data as $file => $lines) {
-            if ($this->filter->isFile($file) && !isset($this->data[$file])) {
+            if ($this->filter->isFile($file) && !isset($this->data[$file]) && !$this->filter()->isFiltered($file)) {
                 $this->data[$file] = array();
 
                 foreach ($lines as $k => $v) {
@@ -591,62 +608,15 @@ private function initializeFilesThatAreSeenTheFirstTime(array $data)
      */
     private function addUncoveredFilesFromWhitelist()
     {
-        $data           = array();
-        $uncoveredFiles = array_diff(
-            $this->filter->getWhitelist(),
-            array_keys($this->data)
-        );
+        $data = [];
 
-        foreach ($uncoveredFiles as $uncoveredFile) {
-            if (!file_exists($uncoveredFile)) {
-                continue;
-            }
-
-            if ($this->processUncoveredFilesFromWhitelist) {
-                $this->processUncoveredFileFromWhitelist(
-                    $uncoveredFile,
-                    $data,
-                    $uncoveredFiles
-                );
-            } else {
-                $data[$uncoveredFile] = array();
-
-                $lines = count(file($uncoveredFile));
-
-                for ($i = 1; $i <= $lines; $i++) {
-                    $data[$uncoveredFile][$i] = PHP_CodeCoverage_Driver::LINE_NOT_EXECUTED;
-                }
-            }
+        foreach (array_keys($this->uncoveredFiles) as $file) {
+            $data[$file] = $this->data[$file];
         }
 
         $this->append($data, 'UNCOVERED_FILES_FROM_WHITELIST');
     }
 
-    /**
-     * @param string $uncoveredFile
-     * @param array  $data
-     * @param array  $uncoveredFiles
-     */
-    private function processUncoveredFileFromWhitelist($uncoveredFile, array &$data, array $uncoveredFiles)
-    {
-        $this->driver->start();
-        include_once $uncoveredFile;
-        $coverage = $this->driver->stop();
-
-        foreach ($coverage as $file => $fileCoverage) {
-            if (!isset($data[$file]) &&
-                in_array($file, $uncoveredFiles)) {
-                foreach (array_keys($fileCoverage) as $key) {
-                    if ($fileCoverage[$key] == PHP_CodeCoverage_Driver::LINE_EXECUTED) {
-                        $fileCoverage[$key] = PHP_CodeCoverage_Driver::LINE_NOT_EXECUTED;
-                    }
-                }
-
-                $data[$file] = $fileCoverage;
-            }
-        }
-    }
-
     /**
      * Returns the lines of a source file that should be ignored.
      *
@@ -917,4 +887,22 @@ private function selectDriver()
             return new PHP_CodeCoverage_Driver_Xdebug;
         }
     }
+
+    /**
+     * Initialise the data with the executable/dead lines from each file in the whitelist
+     */
+    private function initData()
+    {
+        foreach ($this->filter()->getWhitelist() as $file) {
+            $this->driver->start();
+            include_once($file);
+            $data = $this->driver->stop();
+
+            $this->initializeFilesThatAreSeenTheFirstTime($data);
+        }
+
+        foreach (array_keys($this->data) as $file) {
+            $this->uncoveredFiles[$file] = 1;
+        }
+    }
 }
diff --git a/src/CodeCoverage/Driver.php b/src/CodeCoverage/Driver.php
index 8635acefe..4452ec02e 100644
--- a/src/CodeCoverage/Driver.php
+++ b/src/CodeCoverage/Driver.php
@@ -36,7 +36,7 @@ interface PHP_CodeCoverage_Driver
     /**
      * Start collection of code coverage information.
      */
-    public function start();
+    public function start($determineUnusedAndDead = true);
 
     /**
      * Stop collection of code coverage information.
diff --git a/src/CodeCoverage/Driver/HHVM.php b/src/CodeCoverage/Driver/HHVM.php
index a9d8f0cef..4250091a3 100644
--- a/src/CodeCoverage/Driver/HHVM.php
+++ b/src/CodeCoverage/Driver/HHVM.php
@@ -19,7 +19,7 @@ class PHP_CodeCoverage_Driver_HHVM extends PHP_CodeCoverage_Driver_Xdebug
     /**
      * Start collection of code coverage information.
      */
-    public function start()
+    public function start($determineUnusedAndDead = true)
     {
         xdebug_start_code_coverage();
     }
diff --git a/src/CodeCoverage/Driver/PHPDBG.php b/src/CodeCoverage/Driver/PHPDBG.php
index f3eb6214a..4b8f4afe3 100644
--- a/src/CodeCoverage/Driver/PHPDBG.php
+++ b/src/CodeCoverage/Driver/PHPDBG.php
@@ -37,7 +37,7 @@ public function __construct()
     /**
      * Start collection of code coverage information.
      */
-    public function start()
+    public function start($determineUnusedAndDead = true)
     {
         phpdbg_start_oplog();
     }
diff --git a/src/CodeCoverage/Driver/Xdebug.php b/src/CodeCoverage/Driver/Xdebug.php
index 0cd7b9adc..1461569d4 100644
--- a/src/CodeCoverage/Driver/Xdebug.php
+++ b/src/CodeCoverage/Driver/Xdebug.php
@@ -16,6 +16,13 @@
  */
 class PHP_CodeCoverage_Driver_Xdebug implements PHP_CodeCoverage_Driver
 {
+    /**
+     * Cache the number of lines for each file
+     *
+     * @var array
+     */
+    private $cacheNumLines = [];
+
     /**
      * Constructor.
      */
@@ -36,9 +43,13 @@ public function __construct()
     /**
      * Start collection of code coverage information.
      */
-    public function start()
+    public function start($determineUnusedAndDead = true)
     {
-        xdebug_start_code_coverage(XDEBUG_CC_UNUSED | XDEBUG_CC_DEAD_CODE);
+        if ($determineUnusedAndDead) {
+            xdebug_start_code_coverage(XDEBUG_CC_UNUSED | XDEBUG_CC_DEAD_CODE);
+        } else {
+            xdebug_start_code_coverage();
+        }
     }
 
     /**
@@ -85,13 +96,17 @@ private function cleanup(array $data)
      */
     private function getNumberOfLinesInFile($file)
     {
-        $buffer = file_get_contents($file);
-        $lines  = substr_count($buffer, "\n");
+        if (!isset($this->cacheNumLines[$file])) {
+            $buffer = file_get_contents($file);
+            $lines  = substr_count($buffer, "\n");
+
+            if (substr($buffer, -1) !== "\n") {
+                $lines++;
+            }
 
-        if (substr($buffer, -1) !== "\n") {
-            $lines++;
+            $this->cacheNumLines[$file] = $lines;
         }
 
-        return $lines;
+        return $this->cacheNumLines[$file];
     }
 }