diff --git a/CHANGES b/CHANGES
index 7b0b9ca0..b764003e 100644
--- a/CHANGES
+++ b/CHANGES
@@ -11,6 +11,8 @@ LIST OF CHANGES for npg_ranger project
   - upgrade tmp to 0.0.31 from 0.0.30
   - do not allow query strings containing multiple attribute-value pairs
     for the same attribute
+  - added flags to server to change logging level and enable logging to console
+  - all logging to console is now sent to stderr
   - upgrade Freebayes to 1.1.0 from 1.0.2-npg-Aug2016 in TravisCI and docs
 
 release 1.0.0
diff --git a/bin/client.js b/bin/client.js
index be767afa..21cc06fd 100755
--- a/bin/client.js
+++ b/bin/client.js
@@ -65,7 +65,7 @@ cline
   .version(require('../package.json').version)
   .description('Command line client for GA4GH data streaming')
   .arguments('<url> [output]')
-  .option('--debug', 'Show debug output')
+  .option('--loglevel <level>', 'level of logging output', /^(error|warn|info|debug)$/i, 'warn')
   .option('--accept-trailers', 'Request trailers from server')
   .parse(process.argv);
 
@@ -91,11 +91,9 @@ cline.on('--help', () => {
 if ( !cline.args.length ||
      ( cline.args.length != 1 && cline.args.length != 2 ) ) { cline.help(); }
 
-if ( !cline.debug ) {
-  LOGGER.level = 'warn';
-} else {
-  LOGGER.level = 'debug';
-}
+LOGGER.setup(true);
+
+LOGGER.level = cline.loglevel;
 
 var url    = cline.args[0];
 var output = cline.args.length == 2 ? cline.args[1] : undefined;
diff --git a/bin/server.js b/bin/server.js
index d065c5ce..d9bcfae8 100755
--- a/bin/server.js
+++ b/bin/server.js
@@ -247,18 +247,36 @@ class BrokerFactory {
       : new FlatBroker(serverFactory);
   }
 }
+function setLogLevel(options) {
+  if (options.get('debug')) {
+    LOGGER.level = 'debug';
+    return;
+  }
+  let logLevel = options.get('loglevel');
+  let knownLevels = ['error', 'warn', 'info', 'debug', 'silly'];
+  if (knownLevels.indexOf(logLevel) !== -1) {
+    LOGGER.level = logLevel;
+    return;
+  }
+  // --loglevel was given an invalid parameter - leave at default and log error
+  LOGGER.error('configuration: loglevel expects one of ' + knownLevels.join(',') + '; but received ' + logLevel);
+  process.exit(1);
+}
 
 /**
  * Application's main method.
  */
 if ( require.main === module ) {
   const options = config.provide(config.fromCommandLine);
+
   if ( options.get('version') ) {
     console.log(require('../package.json').version);
     process.exit(0);
-  } else if ( options.get('debug') ) {
-    LOGGER.level = 'debug';
+  } else {
+    LOGGER.setup(options.get('logconsole'));
+    setLogLevel(options);
   }
+
   let numWorkers    = options.get('numworkers');
   let waitingConsec = options.get('clustertimeout');
   let maxConsec     = options.get('clustermaxdeaths');
diff --git a/lib/config.js b/lib/config.js
index e4104d6d..cb689e9d 100644
--- a/lib/config.js
+++ b/lib/config.js
@@ -56,12 +56,15 @@ const optionsList = [
   ['s','skipauth'             ,'skip authorisation steps'],
   ['' ,'anyorigin'            ,'accept CORS requests from any origin'],
   ['e','emaildomain=DOMAIN'   ,'email domain to validate the remote user value against'],
-  ['d','debug'                ,'debugging mode for this server'],
+  ['', 'logconsole'           ,'outputs logs to console'],
+  ['d','debug'                ,'sets logger level to debug for this server'],
+  ['L','loglevel=[error|warn|info|debug]','logging level for this server [default: error]'],
   ['V','version'              ,'print version and exit'],
   ['h','help'                 ,'display this help']
 ];
 
 const defaultOptions = {
+  loglevel:         'error',
   [RO_OPTION_KEY]:  false,
   /* cluster */
   numworkers:       1,
diff --git a/lib/logsetup.js b/lib/logsetup.js
index 65f2291f..90a1c935 100644
--- a/lib/logsetup.js
+++ b/lib/logsetup.js
@@ -1,6 +1,7 @@
 "use strict";
 
 const LOGGER = require('winston');
+
 const moment = require('moment');
 
 /**
@@ -27,27 +28,24 @@ var getTimeStamp = function() {
   return moment().format('YYYY-MM-DD HH:mm:ss Z');
 };
 
-try {
-  LOGGER.remove(LOGGER.transports.Console);
-  LOGGER.add(LOGGER.transports.Console, {
-    level:     'warn',
-    colorize:  true,
-    json:      false,
-    timestamp: getTimeStamp,
-    stderrLevels: [ 'error' ] // Which levels to send to stderr
-  });
-  LOGGER.add(LOGGER.transports.File, {
-    level:    'warn',
-    filename: 'npg_ranger.winston.log',
-    json:      false,
-    timestamp: getTimeStamp,
-    maxsize:   10 * 1000 * 1000,
-    maxFiles:  20
-  });
-} catch (e) {
-  console.error('Error when trying to init logging with Winston');
-  console.error(e);
-  process.exit(1);
-}
+var setup = function(logconsole) {
+  try {
+    LOGGER.remove(LOGGER.transports.Console);
+    if (logconsole) {
+      LOGGER.add(LOGGER.transports.Console, {
+        level:        'warn',
+        colorize:     true,
+        json:         false,
+        timestamp:    getTimeStamp,
+        stderrLevels: [ 'error', 'warn', 'info', 'verbose', 'debug', 'silly' ] // Which levels to send to stderr
+      });
+    }
+  } catch (e) {
+    console.error('Error when trying to init logging with Winston');
+    console.error(e);
+    process.exit(1);
+  }
+};
 
 module.exports = LOGGER;
+module.exports.setup = setup;
diff --git a/test/client/highLevelClient.spec.js b/test/client/highLevelClient.spec.js
index 6cfd686d..bf0dcf66 100644
--- a/test/client/highLevelClient.spec.js
+++ b/test/client/highLevelClient.spec.js
@@ -241,6 +241,7 @@ describe('Running with ranger server with a', () => {
     let serv = spawn(serverCommand, [
       '-s',
       '-d',
+      '--logconsole',
       '-n0',
       `-p${SERV_PORT}`,
       `-m${mongourl}`]);
@@ -256,7 +257,7 @@ describe('Running with ranger server with a', () => {
   it('file url', (done) => {
     let serv = startServer( done, fail );
 
-    serv.stdout.on('data', (data) => {
+    serv.stderr.on('data', (data) => {
       if (data.toString().match(/Server listening on /)) {
         // Server is listening and ready for connection
         let client = spawn('bin/client.js', [
@@ -278,7 +279,7 @@ describe('Running with ranger server with a', () => {
   it('sample url', (done) => {
     let serv = startServer( done, fail );
 
-    serv.stdout.on('data', (data) => {
+    serv.stderr.on('data', (data) => {
       if (data.toString().match(/Server listening on /)) {
         // Server is listening and ready for connection
         let client = spawn('bin/client.js', [
@@ -304,7 +305,7 @@ describe('Running with ranger server with a', () => {
   it('sample url returning vcf', (done) => {
     let serv = startServer( done, fail );
 
-    serv.stdout.on('data', (data) => {
+    serv.stderr.on('data', (data) => {
       if (data.toString().match(/Server listening on /)) {
         // Server is listening and ready for connection
         let body = '';
@@ -327,7 +328,7 @@ describe('Running with ranger server with a', () => {
   it('GA4GH url and the redirect is followed', (done) => {
     let serv = startServer( done, fail );
 
-    serv.stdout.on('data', (data) => {
+    serv.stderr.on('data', (data) => {
       if (data.toString().match(/Server listening on /)) {
         // Server is listening and ready for connection
         let client = spawn('bin/client.js', [
diff --git a/test/config.spec.js b/test/config.spec.js
index 9ff5c1b2..e6cc29b9 100644
--- a/test/config.spec.js
+++ b/test/config.spec.js
@@ -131,6 +131,8 @@ describe('Listing config options', function() {
       'debug=true',
       'emaildomain="some.com"',
       'hostname="myhost"',
+      'logconsole=undefined',
+      'loglevel="error"',
       'mongourl="mymongourl"',
       'multiref=undefined',
       'numworkers=3',
diff --git a/test/server/secure_server.spec.js b/test/server/secure_server.spec.js
index d6b46c64..b9ff33b3 100644
--- a/test/server/secure_server.spec.js
+++ b/test/server/secure_server.spec.js
@@ -35,6 +35,7 @@ describe('test running https server', () => {
     let s = spawn(serverCommand, [
       '-s',
       '-d',
+      '--logconsole',
       '--startssl',
       '--secure_key', private_pem,
       '--secure_cert', cert_pem,
@@ -106,7 +107,7 @@ describe('test running https server', () => {
   it('can reply with a reference from a https requests', ( done ) => {
     serv = startServer( done );
     let acc  = 'XYZ120923';
-    serv.stdout.on('data', (data) => {
+    serv.stderr.on('data', (data) => {
       if (data.toString().match(/Server listening on /)) {
         // Server is listening and ready for connection
         let options = {