diff --git a/CHANGELOG.md b/CHANGELOG.md
index 61765affb..846cac2fc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,5 @@
+* Fixed: Using toggle comment shortcut respects indentation level
+
 * Fixed: Search never completing in the command panel
 
 * Fixed: cmd-n now works when no windows are open
diff --git a/spec/app/edit-session-spec.coffee b/spec/app/edit-session-spec.coffee
index e9e74dd52..47f8ac23d 100644
--- a/spec/app/edit-session-spec.coffee
+++ b/spec/app/edit-session-spec.coffee
@@ -1717,10 +1717,10 @@ describe "EditSession", ->
         editSession.setSelectedBufferRange([[4, 5], [7, 5]])
         editSession.toggleLineCommentsInSelection()
 
-        expect(buffer.lineForRow(4)).toBe "//     while(items.length > 0) {"
-        expect(buffer.lineForRow(5)).toBe "//       current = items.shift();"
-        expect(buffer.lineForRow(6)).toBe "//       current < pivot ? left.push(current) : right.push(current);"
-        expect(buffer.lineForRow(7)).toBe "//     }"
+        expect(buffer.lineForRow(4)).toBe "    // while(items.length > 0) {"
+        expect(buffer.lineForRow(5)).toBe "    //   current = items.shift();"
+        expect(buffer.lineForRow(6)).toBe "    //   current < pivot ? left.push(current) : right.push(current);"
+        expect(buffer.lineForRow(7)).toBe "    // }"
         expect(editSession.getSelectedBufferRange()).toEqual [[4, 8], [7, 8]]
 
         editSession.toggleLineCommentsInSelection()
@@ -1732,9 +1732,9 @@ describe "EditSession", ->
       it "does not comment the last line of a non-empty selection if it ends at column 0", ->
         editSession.setSelectedBufferRange([[4, 5], [7, 0]])
         editSession.toggleLineCommentsInSelection()
-        expect(buffer.lineForRow(4)).toBe "//     while(items.length > 0) {"
-        expect(buffer.lineForRow(5)).toBe "//       current = items.shift();"
-        expect(buffer.lineForRow(6)).toBe "//       current < pivot ? left.push(current) : right.push(current);"
+        expect(buffer.lineForRow(4)).toBe "    // while(items.length > 0) {"
+        expect(buffer.lineForRow(5)).toBe "    //   current = items.shift();"
+        expect(buffer.lineForRow(6)).toBe "    //   current < pivot ? left.push(current) : right.push(current);"
         expect(buffer.lineForRow(7)).toBe "    }"
 
       it "uncomments lines if all lines match the comment regex", ->
diff --git a/spec/app/language-mode-spec.coffee b/spec/app/language-mode-spec.coffee
index efb45b138..be7ebb14f 100644
--- a/spec/app/language-mode-spec.coffee
+++ b/spec/app/language-mode-spec.coffee
@@ -14,19 +14,27 @@ describe "LanguageMode", ->
       editSession = project.open('sample.js', autoIndent: false)
       {buffer, languageMode} = editSession
 
+    describe ".minIndentLevelForRowRange(startRow, endRow)", ->
+      it "returns the minimum indent level for the given row range", ->
+        expect(languageMode.minIndentLevelForRowRange(4, 7)).toBe 2
+        expect(languageMode.minIndentLevelForRowRange(5, 7)).toBe 2
+        expect(languageMode.minIndentLevelForRowRange(5, 6)).toBe 3
+        expect(languageMode.minIndentLevelForRowRange(9, 11)).toBe 1
+        expect(languageMode.minIndentLevelForRowRange(10, 10)).toBe 0
+
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
         languageMode.toggleLineCommentsForBufferRows(4, 7)
-        expect(buffer.lineForRow(4)).toBe "//     while(items.length > 0) {"
-        expect(buffer.lineForRow(5)).toBe "//       current = items.shift();"
-        expect(buffer.lineForRow(6)).toBe "//       current < pivot ? left.push(current) : right.push(current);"
-        expect(buffer.lineForRow(7)).toBe "//     }"
+        expect(buffer.lineForRow(4)).toBe "    // while(items.length > 0) {"
+        expect(buffer.lineForRow(5)).toBe "    //   current = items.shift();"
+        expect(buffer.lineForRow(6)).toBe "    //   current < pivot ? left.push(current) : right.push(current);"
+        expect(buffer.lineForRow(7)).toBe "    // }"
 
         languageMode.toggleLineCommentsForBufferRows(4, 5)
         expect(buffer.lineForRow(4)).toBe "    while(items.length > 0) {"
         expect(buffer.lineForRow(5)).toBe "      current = items.shift();"
-        expect(buffer.lineForRow(6)).toBe "//       current < pivot ? left.push(current) : right.push(current);"
-        expect(buffer.lineForRow(7)).toBe "//     }"
+        expect(buffer.lineForRow(6)).toBe "    //   current < pivot ? left.push(current) : right.push(current);"
+        expect(buffer.lineForRow(7)).toBe "    // }"
 
     describe "fold suggestion", ->
       describe ".doesBufferRowStartFold(bufferRow)", ->
@@ -58,17 +66,28 @@ describe "LanguageMode", ->
 
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
-        languageMode.toggleLineCommentsForBufferRows(4, 7)
-        expect(buffer.lineForRow(4)).toBe "#     pivot = items.shift()"
-        expect(buffer.lineForRow(5)).toBe "#     left = []"
-        expect(buffer.lineForRow(6)).toBe "#     right = []"
-        expect(buffer.lineForRow(7)).toBe "# "
+        languageMode.toggleLineCommentsForBufferRows(4, 6)
+        expect(buffer.lineForRow(4)).toBe "    # pivot = items.shift()"
+        expect(buffer.lineForRow(5)).toBe "    # left = []"
+        expect(buffer.lineForRow(6)).toBe "    # right = []"
 
         languageMode.toggleLineCommentsForBufferRows(4, 5)
         expect(buffer.lineForRow(4)).toBe "    pivot = items.shift()"
         expect(buffer.lineForRow(5)).toBe "    left = []"
-        expect(buffer.lineForRow(6)).toBe "#     right = []"
-        expect(buffer.lineForRow(7)).toBe "# "
+        expect(buffer.lineForRow(6)).toBe "    # right = []"
+
+      it "comments/uncomments lines when empty line", ->
+        languageMode.toggleLineCommentsForBufferRows(4, 7)
+        expect(buffer.lineForRow(4)).toBe "    # pivot = items.shift()"
+        expect(buffer.lineForRow(5)).toBe "    # left = []"
+        expect(buffer.lineForRow(6)).toBe "    # right = []"
+        expect(buffer.lineForRow(7)).toBe "    # "
+
+        languageMode.toggleLineCommentsForBufferRows(4, 5)
+        expect(buffer.lineForRow(4)).toBe "    pivot = items.shift()"
+        expect(buffer.lineForRow(5)).toBe "    left = []"
+        expect(buffer.lineForRow(6)).toBe "    # right = []"
+        expect(buffer.lineForRow(7)).toBe "    # "
 
     describe "fold suggestion", ->
       describe ".doesBufferRowStartFold(bufferRow)", ->
diff --git a/src/app/language-mode.coffee b/src/app/language-mode.coffee
index 204e3f7ef..9bf809f9d 100644
--- a/src/app/language-mode.coffee
+++ b/src/app/language-mode.coffee
@@ -81,8 +81,10 @@ class LanguageMode
             columnEnd = columnStart + match[2].length
             buffer.change([[row, columnStart], [row, columnEnd]], "")
       else
+        indent = @minIndentLevelForRowRange(start, end)
+        indentString = @editSession.buildIndentString(indent)
         for row in [start..end]
-          buffer.insert([row, 0], commentStartString)
+          buffer.change([[row, 0], [row, indentString.length]], indentString + commentStartString)
 
   # Folds all the foldable lines in the buffer.
   foldAll: ->
@@ -180,6 +182,17 @@ class LanguageMode
 
     desiredIndentLevel
 
+  # Calculate a minimum indent level for a range of lines excluding empty lines.
+  #
+  # startRow - The row {Number} to start at
+  # endRow - The row {Number} to end at
+  #
+  # Returns a {Number} of the indent level of the block of lines.
+  minIndentLevelForRowRange: (startRow, endRow) ->
+    indents = (@editSession.indentationForBufferRow(row) for row in [startRow..endRow] when not @editSession.isBufferRowBlank(row))
+    indents = [0] unless indents.length
+    Math.min(indents...)
+
   # Indents all the rows between two buffer row numbers.
   #
   # startRow - The row {Number} to start at