diff --git a/lib/rules/no-multiple-empty-lines.js b/lib/rules/no-multiple-empty-lines.js
index daab826f4c3d..96b043918938 100644
--- a/lib/rules/no-multiple-empty-lines.js
+++ b/lib/rules/no-multiple-empty-lines.js
@@ -17,6 +17,8 @@ module.exports = {
             recommended: false
         },
 
+        fixable: "whitespace",
+
         schema: [
             {
                 type: "object",
@@ -76,21 +78,34 @@ module.exports = {
 
             "Program:exit": function checkBlankLines(node) {
                 var lines = sourceCode.lines,
-                    currentLocation = -1,
-                    lastLocation,
+                    fullLines = sourceCode.text.match(/.*(\r\n|\r|\n|\u2028|\u2029)/g),
+                    firstNonBlankLine = -1,
+                    trimmedLines = [],
+                    linesRangeStart = [],
                     blankCounter = 0,
+                    currentLocation,
+                    lastLocation,
                     location,
                     firstOfEndingBlankLines,
-                    firstNonBlankLine = -1,
-                    trimmedLines = [];
+                    diff,
+                    fix,
+                    rangeStart,
+                    rangeEnd;
+
+                fix = function(fixer) {
+                    return fixer.removeRange([rangeStart, rangeEnd]);
+                };
 
+                linesRangeStart.push(0);
                 lines.forEach(function(str, i) {
-                    var trimmed = str.trim();
+                    var length = i < fullLines.length ? fullLines[i].length : 0,
+                        trimmed = str.trim();
 
                     if ((firstNonBlankLine === -1) && (trimmed !== "")) {
                         firstNonBlankLine = i;
                     }
 
+                    linesRangeStart.push(linesRangeStart[linesRangeStart.length - 1] + length);
                     trimmedLines.push(trimmed);
                 });
 
@@ -122,8 +137,15 @@ module.exports = {
 
                 // Aggregate and count blank lines
                 if (firstNonBlankLine > maxBOF) {
-                    context.report(node, 0,
-                            "Too many blank lines at the beginning of file. Max of " + maxBOF + " allowed.");
+                    diff = firstNonBlankLine - maxBOF;
+                    rangeStart = linesRangeStart[firstNonBlankLine - diff];
+                    rangeEnd = linesRangeStart[firstNonBlankLine];
+                    context.report({
+                        node: node,
+                        loc: node.loc.start,
+                        message: "Too many blank lines at the beginning of file. Max of " + maxBOF + " allowed.",
+                        fix: fix
+                    });
                 }
                 currentLocation = firstNonBlankLine - 1;
 
@@ -144,20 +166,29 @@ module.exports = {
 
                             // within the file, not at the end
                             if (blankCounter >= max) {
+                                diff = blankCounter - max + 1;
+                                rangeStart = linesRangeStart[location.line - diff];
+                                rangeEnd = linesRangeStart[location.line];
+
                                 context.report({
                                     node: node,
                                     loc: location,
-                                    message: "More than " + max + " blank " + (max === 1 ? "line" : "lines") + " not allowed."
+                                    message: "More than " + max + " blank " + (max === 1 ? "line" : "lines") + " not allowed.",
+                                    fix: fix
                                 });
                             }
                         } else {
 
                             // inside the last blank lines
                             if (blankCounter > maxEOF) {
+                                diff = blankCounter - maxEOF + 1;
+                                rangeStart = linesRangeStart[location.line - diff];
+                                rangeEnd = linesRangeStart[location.line - 1];
                                 context.report({
                                     node: node,
                                     loc: location,
-                                    message: "Too many blank lines at the end of file. Max of " + maxEOF + " allowed."
+                                    message: "Too many blank lines at the end of file. Max of " + maxEOF + " allowed.",
+                                    fix: fix
                                 });
                             }
                         }
diff --git a/tests/lib/rules/no-multiple-empty-lines.js b/tests/lib/rules/no-multiple-empty-lines.js
index 428dc98aac62..08c3d4020022 100644
--- a/tests/lib/rules/no-multiple-empty-lines.js
+++ b/tests/lib/rules/no-multiple-empty-lines.js
@@ -116,6 +116,10 @@ ruleTester.run("no-multiple-empty-lines", rule, {
             code: "\n// valid 11\nvar a = 1;\n",
             options: [{ max: 2, maxBOF: 1 }]
         },
+        {
+            code: "// valid 12\r\n// windows line endings\r\nvar a = 5;\r\nvar b = 3;\r\n\r\n",
+            options: [ { max: 1 } ]
+        },
 
         // template strings
         {
@@ -151,99 +155,130 @@ ruleTester.run("no-multiple-empty-lines", rule, {
     invalid: [
         {
             code: "// invalid 1\nvar a = 5;\n\n\nvar b = 3;",
+            output: "// invalid 1\nvar a = 5;\n\nvar b = 3;",
             errors: [ getExpectedError(1) ],
             options: [ { max: 1 } ]
         },
         {
             code: "// invalid 2\n\n\n\n\nvar a = 5;",
+            output: "// invalid 2\n\n\nvar a = 5;",
             errors: [ getExpectedError(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 3\nvar a = 5;\n\n\n\n",
+            output: "// invalid 3\nvar a = 5;\n\n\n",
             errors: [ getExpectedErrorEOF(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 4\nvar a = 5;\n \n \n \n",
+            output: "// invalid 4\nvar a = 5;\n \n \n",
             errors: [ getExpectedErrorEOF(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 5\nvar a=5;\n\n\n\nvar b = 3;",
+            output: "// invalid 5\nvar a=5;\n\n\nvar b = 3;",
             errors: [ getExpectedError(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 6\nvar a=5;\n\n\n\nvar b = 3;\n",
+            output: "// invalid 6\nvar a=5;\n\n\nvar b = 3;\n",
             errors: [ getExpectedError(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 7\nvar a = 5;\n\n\n\nb = 3;\nvar c = 5;\n\n\n\nvar d = 3;",
+            output: "// invalid 7\nvar a = 5;\n\n\nb = 3;\nvar c = 5;\n\n\nvar d = 3;",
             errors: 2,
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 8\nvar a = 5;\n\n\n\n\n\n\n\n\n\n\n\n\n\nb = 3;",
+            output: "// invalid 8\nvar a = 5;\n\n\nb = 3;",
             errors: [ getExpectedError(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 9\nvar a=5;\n\n\n\n\n",
+            output: "// invalid 9\nvar a=5;\n\n\n",
             errors: [ getExpectedErrorEOF(2) ],
             options: [ { max: 2 } ]
         },
         {
             code: "// invalid 10\nvar a = 5;\n\nvar b = 3;",
+            output: "// invalid 10\nvar a = 5;\nvar b = 3;",
             errors: [ getExpectedError(0) ],
             options: [ { max: 0 } ]
         },
         {
             code: "// invalid 11\nvar a = 5;\n\n\n",
+            output: "// invalid 11\nvar a = 5;\n\n",
             errors: [ getExpectedErrorEOF(1) ],
             options: [ { max: 5, maxEOF: 1 } ]
         },
         {
             code: "// invalid 12\nvar a = 5;\n\n\n\n\n\n",
+            output: "// invalid 12\nvar a = 5;\n\n\n\n\n",
             errors: [ getExpectedErrorEOF(4) ],
             options: [ { max: 0, maxEOF: 4 } ]
         },
         {
             code: "// invalid 13\n\n\n\n\n\n\n\n\nvar a = 5;\n\n\n",
+            output: "// invalid 13\n\n\n\n\n\n\n\n\nvar a = 5;\n\n",
             errors: [ getExpectedErrorEOF(1) ],
             options: [ { max: 10, maxEOF: 1 } ]
         },
         {
             code: "// invalid 14\nvar a = 5;\n\n",
+            output: "// invalid 14\nvar a = 5;\n",
             errors: [ getExpectedErrorEOF(0) ],
             options: [ { max: 2, maxEOF: 0 } ]
         },
         {
             code: "\n\n// invalid 15\nvar a = 5;\n",
+            output: "\n// invalid 15\nvar a = 5;\n",
             errors: [ getExpectedErrorBOF(1) ],
             options: [ { max: 5, maxBOF: 1 } ]
         },
         {
             code: "\n\n\n\n\n// invalid 16\nvar a = 5;\n",
+            output: "\n\n\n\n// invalid 16\nvar a = 5;\n",
             errors: [ getExpectedErrorBOF(4)],
             options: [ { max: 0, maxBOF: 4 } ]
         },
         {
             code: "\n\n// invalid 17\n\n\n\n\n\n\n\n\nvar a = 5;\n",
+            output: "\n// invalid 17\n\n\n\n\n\n\n\n\nvar a = 5;\n",
             errors: [ getExpectedErrorBOF(1) ],
             options: [ { max: 10, maxBOF: 1 } ]
         },
         {
             code: "\n// invalid 18\nvar a = 5;\n",
+            output: "// invalid 18\nvar a = 5;\n",
             errors: [ getExpectedErrorBOF(0) ],
             options: [ { max: 2, maxBOF: 0 } ]
         },
         {
             code: "\n\n\n// invalid 19\nvar a = 5;\n\n",
+            output: "// invalid 19\nvar a = 5;\n",
             errors: [ getExpectedErrorBOF(0),
                       getExpectedErrorEOF(0) ],
             options: [ { max: 2, maxBOF: 0, maxEOF: 0 } ]
+        },
+        {
+            code: "// invalid 20\r\n// windows line endings\r\nvar a = 5;\r\nvar b = 3;\r\n\r\n\r\n",
+            output: "// invalid 20\r\n// windows line endings\r\nvar a = 5;\r\nvar b = 3;\r\n\r\n",
+            errors: [ getExpectedErrorEOF(1) ],
+            options: [ { max: 1 } ]
+        },
+        {
+            code: "// invalid 21\n// unix line endings\nvar a = 5;\nvar b = 3;\n\n\n",
+            output: "// invalid 21\n// unix line endings\nvar a = 5;\nvar b = 3;\n\n",
+            errors: [ getExpectedErrorEOF(1) ],
+            options: [ { max: 1 } ]
         }
     ]
 });