diff --git a/lib/jsduck/js_parser.rb b/lib/jsduck/js_parser.rb
index 36e705ae9f5c3a0130c0fef86367c946848952f0..25bf26b1b81df7ba4fb2a5067eca05227b1ea812 100644
--- a/lib/jsduck/js_parser.rb
+++ b/lib/jsduck/js_parser.rb
@@ -155,7 +155,7 @@ module JsDuck
       properties = NODE_TYPES[node["type"]]
 
       unless properties
-        puts "Unknown node type: "+node["type"]
+        $stderr.puts "Unknown node type: "+node["type"]
         exit(1)
       end
 
diff --git a/lib/jsduck/json_duck.rb b/lib/jsduck/json_duck.rb
index d7d15bf17e92578bb45a80485ec249b14908a590..3809a494d354afd51dcfdc9e5c4d4cde0f67d77a 100644
--- a/lib/jsduck/json_duck.rb
+++ b/lib/jsduck/json_duck.rb
@@ -37,7 +37,7 @@ module JsDuck
       begin
         self.parse(JsDuck::IO.read(filename))
       rescue
-        puts "Oh noes!  #{filename} is not a valid JSON file."
+        $stderr.puts "Oh noes!  #{filename} is not a valid JSON file."
         exit(1)
       end
     end
diff --git a/lib/jsduck/logger.rb b/lib/jsduck/logger.rb
index 241fba8d7b38919b3db0dbd3688191213fab6eaf..71fdb719dfa28ac53d025b2a9c40dbcac0677a69 100644
--- a/lib/jsduck/logger.rb
+++ b/lib/jsduck/logger.rb
@@ -57,7 +57,7 @@ module JsDuck
     # Prints log message with optional filename appended
     def log(msg, filename=nil)
       if @verbose
-        puts paint(:green, msg) + " " + format(filename) + " ..."
+        $stderr.puts paint(:green, msg) + " " + format(filename) + " ..."
       end
     end
 
@@ -121,10 +121,10 @@ module JsDuck
     # Prints fatal error message with backtrace.
     # The error param should be $! from resque block.
     def fatal(msg, error)
-      puts "#{paint(:red, msg)}: #{error}"
-      puts
-      puts "Here's a full backtrace:"
-      puts error.backtrace
+      $stderr.puts "#{paint(:red, msg)}: #{error}"
+      $stderr.puts
+      $stderr.puts "Here's a full backtrace:"
+      $stderr.puts error.backtrace
     end
 
     private
diff --git a/lib/jsduck/options.rb b/lib/jsduck/options.rb
index 79126454adf9b55199afe582f848c6d60043e41b..de5b90a59569cef083c466f8bb163d73810c0bd8 100644
--- a/lib/jsduck/options.rb
+++ b/lib/jsduck/options.rb
@@ -397,7 +397,7 @@ module JsDuck
           if File.exists?(path)
             config = read_json_config(path)
           else
-            puts "Oh noes!  The config file #{path} doesn't exist."
+            $stderr.puts "Oh noes!  The config file #{path} doesn't exist."
             exit(1)
           end
           # treat paths inside JSON config relative to the location of
@@ -520,35 +520,35 @@ module JsDuck
     # Runs checks on the options
     def validate
       if @input_files.length == 0 && !@welcome && !@guides && !@videos && !@examples
-        puts "You should specify some input files, otherwise there's nothing I can do :("
+        $stderr.puts "You should specify some input files, otherwise there's nothing I can do :("
         exit(1)
       elsif @output_dir == :stdout && !@export
-        puts "Output to STDOUT only works when using --export option."
+        $stderr.puts "Output to STDOUT only works when using --export option."
         exit(1)
       elsif ![nil, :full, :api, :examples].include?(@export)
-        puts "Unknown export format: #{@export}"
+        $stderr.puts "Unknown export format: #{@export}"
         exit(1)
       elsif @output_dir != :stdout
         if !@output_dir
-          puts "You should also specify an output directory, where I could write all this amazing documentation."
+          $stderr.puts "You should also specify an output directory, where I could write all this amazing documentation."
           exit(1)
         elsif File.exists?(@output_dir) && !File.directory?(@output_dir)
-          puts "Oh noes!  The output directory is not really a directory at all :("
+          $stderr.puts "Oh noes!  The output directory is not really a directory at all :("
           exit(1)
         elsif !File.exists?(File.dirname(@output_dir))
-          puts "Oh noes!  The parent directory for #{@output_dir} doesn't exist."
+          $stderr.puts "Oh noes!  The parent directory for #{@output_dir} doesn't exist."
           exit(1)
         elsif !@export && !File.exists?(@template_dir + "/extjs")
-          puts "Oh noes!  The template directory does not contain extjs/ directory :("
-          puts "Please copy ExtJS over to template/extjs or create symlink."
-          puts "For example:"
-          puts "    $ cp -r /path/to/ext-4.0.0 " + @template_dir + "/extjs"
+          $stderr.puts "Oh noes!  The template directory does not contain extjs/ directory :("
+          $stderr.puts "Please copy ExtJS over to template/extjs or create symlink."
+          $stderr.puts "For example:"
+          $stderr.puts "    $ cp -r /path/to/ext-4.0.0 " + @template_dir + "/extjs"
           exit(1)
         elsif !@export && !File.exists?(@template_dir + "/resources/css")
-          puts "Oh noes!  CSS files for custom ExtJS theme missing :("
-          puts "Please compile SASS files in template/resources/sass with compass."
-          puts "For example:"
-          puts "    $ compass compile " + @template_dir + "/resources/sass"
+          $stderr.puts "Oh noes!  CSS files for custom ExtJS theme missing :("
+          $stderr.puts "Please compile SASS files in template/resources/sass with compass."
+          $stderr.puts "For example:"
+          $stderr.puts "    $ compass compile " + @template_dir + "/resources/sass"
           exit(1)
         end
       end