diff --git a/docs/instrument.md b/docs/instrument.md
index 06126b992..f0a6d3bf8 100644
--- a/docs/instrument.md
+++ b/docs/instrument.md
@@ -18,6 +18,9 @@ nyc instrument <input> [output]
 The `[output]` directory is optional and can be located anywhere, if not set the instrumented code will be sent to `stdout`.
 For example, `nyc instrument . ./output` will produce instrumented versions of any source files it finds in `.` and store them in `./output`.
 
+The `--baseline` option will save a baseline coverage file to `<temp-dir>/baseline/coverage.json`.
+Include this file when reporting to highlight files with no test coverage.
+
 The `--delete` option will remove the existing output directory before instrumenting.
 
 The `--in-place` option will allow you to run the instrument command.
diff --git a/index.js b/index.js
index 6d74d0831..2d7b31ef2 100755
--- a/index.js
+++ b/index.js
@@ -48,6 +48,7 @@ class NYC {
 
     this.subprocessBin = config.subprocessBin || path.resolve(__dirname, './bin/nyc.js')
     this._tempDirectory = config.tempDirectory || config.tempDir || './.nyc_output'
+    this._baselineDirectoryName = 'baseline'
     this._instrumenterLib = require(config.instrumenter || './lib/instrumenters/istanbul')
     this._reportDir = config.reportDir || 'coverage'
     this._sourceMap = typeof config.sourceMap === 'boolean' ? config.sourceMap : true
@@ -170,7 +171,7 @@ class NYC {
     return source
   }
 
-  async addAllFiles () {
+  async addAllFiles (coverageFilename) {
     this._loadAdditionalModules()
 
     this.fakeRequire = true
@@ -190,7 +191,7 @@ class NYC {
     })
     this.fakeRequire = false
 
-    this.writeCoverageFile()
+    this.writeCoverageFile(coverageFilename)
   }
 
   async instrumentAllFiles (input, output) {
@@ -335,6 +336,10 @@ class NYC {
       await mkdirp(this.cacheDirectory)
     }
 
+    if (this.config.baseline) {
+      await mkdirp(this.baselineDirectory())
+    }
+
     await mkdirp(this.processInfo.directory)
   }
 
@@ -374,26 +379,25 @@ class NYC {
     return this
   }
 
-  writeCoverageFile () {
-    var coverage = coverageFinder()
+  writeCoverageFile (filename = this.processInfo.uuid) {
+    const coverage = coverageFinder()
 
     // Remove any files that should be excluded but snuck into the coverage
-    Object.keys(coverage).forEach(function (absFile) {
+    Object.keys(coverage).forEach(absFile => {
       if (!this.exclude.shouldInstrument(absFile)) {
         delete coverage[absFile]
       }
-    }, this)
+    })
 
     if (this.cache) {
-      Object.keys(coverage).forEach(function (absFile) {
+      Object.keys(coverage).forEach(absFile => {
         if (this.hashCache[absFile] && coverage[absFile]) {
           coverage[absFile].contentHash = this.hashCache[absFile]
         }
-      }, this)
+      })
     }
 
-    var id = this.processInfo.uuid
-    var coverageFilename = path.resolve(this.tempDirectory(), id + '.json')
+    const coverageFilename = path.resolve(this.tempDirectory(), `${filename}.json`)
 
     fs.writeFileSync(
       coverageFilename,
@@ -516,6 +520,10 @@ class NYC {
     return path.resolve(this.cwd, this._tempDirectory)
   }
 
+  baselineDirectory () {
+    return path.resolve(this.cwd, this._tempDirectory, this._baselineDirectoryName)
+  }
+
   reportDirectory () {
     return path.resolve(this.cwd, this._reportDir)
   }
diff --git a/lib/commands/instrument.js b/lib/commands/instrument.js
index cabb43775..944b0c658 100644
--- a/lib/commands/instrument.js
+++ b/lib/commands/instrument.js
@@ -59,5 +59,14 @@ exports.handler = cliWrapper(async argv => {
     })
   }
 
+  if (argv.baseline) {
+    if (argv.clean) {
+      await nyc.reset()
+    } else {
+      await nyc.createTempDirectory()
+    }
+    await nyc.addAllFiles('baseline/coverage')
+  }
+
   await nyc.instrumentAllFiles(argv.input, argv.output)
 })
diff --git a/test/instrument.js b/test/instrument.js
index 284c2f1cb..2d02d509b 100644
--- a/test/instrument.js
+++ b/test/instrument.js
@@ -353,3 +353,52 @@ t.test('aborts if trying to clean outside working directory', async t => {
   t.strictEqual(status, 1)
   t.match(stderr, /attempt to delete/)
 })
+
+t.test('can produce baseline coverage if `--baseline` is set', async t => {
+  const { status } = await runNYC({
+    args: [
+      'instrument',
+      '--baseline',
+      './input-dir',
+      './output-dir'
+    ],
+    cwd: subdir
+  })
+
+  t.strictEqual(status, 0)
+  const target = path.resolve(subdir, 'output-dir', 'index.js')
+  t.match(await fs.readFile(target, 'utf8'), /console.log\('Hello, World!'\)/)
+  const baseline = path.resolve(fixturesCLI, '.nyc_output', 'baseline', 'coverage.json')
+  t.match(await fs.readFile(baseline, 'utf8'), /statementMap/)
+})
+
+t.test('can skip cleaning if `--no-clean` is set during baseline', async t => {
+  const args = [
+    'instrument',
+    '--baseline',
+    './input-dir',
+    './output-dir'
+  ]
+  const cwd = subdir
+
+  const { status: cleanStatus } = await runNYC({ args, cwd })
+
+  t.strictEqual(cleanStatus, 0)
+  const target = path.resolve(subdir, 'output-dir', 'index.js')
+  t.match(await fs.readFile(target, 'utf8'), /console.log\('Hello, World!'\)/)
+  const baseline = path.resolve(fixturesCLI, '.nyc_output', 'baseline', 'coverage.json')
+  t.match(await fs.readFile(baseline, 'utf8'), /statementMap/)
+
+  args.splice(2, 0, '--no-clean')
+  const { status: noCleanStatus } = await runNYC({ args, cwd })
+
+  t.strictEqual(noCleanStatus, 0)
+
+  const baselineDir = path.resolve(fixturesCLI, '.nyc_output', 'baseline')
+  const processinfoDir = path.resolve(fixturesCLI, '.nyc_output', 'processinfo')
+
+  const baselineFiles = await fs.readdir(baselineDir)
+  const processinfoFiles = await fs.readdir(processinfoDir)
+  t.equal(baselineFiles.length, 1)
+  t.equal(processinfoFiles.length, 2)
+})