diff --git a/docs/source/config_file.rst b/docs/source/config_file.rst
index c34f23d9e169..e98137158bb2 100644
--- a/docs/source/config_file.rst
+++ b/docs/source/config_file.rst
@@ -195,6 +195,24 @@ section of the command line docs.
 
     This option may only be set in the global section (``[mypy]``).
 
+.. confval:: modules
+
+    :type: comma-separated list of strings
+
+    A comma-separated list of modules to be type checked. See the
+    corresponding flag :option:`--module <mypy --module>` for more information.
+
+    This option may only be set in the global section (``[mypy]``).
+
+.. confval:: packages
+
+    :type: comma-separated list of strings
+
+    A comma-separated list of packages to be type checked. See the
+    corresponding flag :option:`--package <mypy --package>` for more information.
+    
+    This option may only be set in the global section (``[mypy]``).
+
 .. confval:: exclude
 
     :type: newline separated list of regular expressions
diff --git a/mypy/config_parser.py b/mypy/config_parser.py
index 5dd8fef2523d..4498b34db34f 100644
--- a/mypy/config_parser.py
+++ b/mypy/config_parser.py
@@ -110,6 +110,8 @@ def check_follow_imports(choice: str) -> str:
     'custom_typeshed_dir': expand_path,
     'mypy_path': lambda s: [expand_path(p.strip()) for p in re.split('[,:]', s)],
     'files': split_and_match_files,
+    'packages': lambda s: [p.strip() for p in s.split(',')],
+    'modules': lambda s: [p.strip() for p in s.split(',')],
     'quickstart_file': expand_path,
     'junit_xml': expand_path,
     # These two are for backwards compatibility
@@ -426,6 +428,12 @@ def parse_section(prefix: str, template: Options,
                 if 'follow_imports' not in results:
                     results['follow_imports'] = 'error'
         results[options_key] = v
+        if key in ('files', 'packages', 'modules'):
+            if (('packages' in results or 'modules' in results) and results.get('files')):
+                print("May only specify one of: module/package or files. Ignoring key:", key,
+                      file=stderr)
+                del results[options_key]
+                continue
     return results, report_dirs
 
 
diff --git a/mypy/main.py b/mypy/main.py
index d7a0e7c52619..862c9737a1d8 100644
--- a/mypy/main.py
+++ b/mypy/main.py
@@ -943,8 +943,13 @@ def set_strict_flags() -> None:
 
     # Paths listed in the config file will be ignored if any paths, modules or packages
     # are passed on the command line.
-    if options.files and not (special_opts.files or special_opts.packages or special_opts.modules):
-        special_opts.files = options.files
+    if not (special_opts.files or special_opts.packages or special_opts.modules):
+        if options.files:
+            special_opts.files = options.files
+        if options.modules:
+            special_opts.modules = options.modules
+        if options.packages:
+            special_opts.packages = options.packages
 
     # Check for invalid argument combinations.
     if require_targets:
diff --git a/mypy/options.py b/mypy/options.py
index 58278b1580e8..f1e1ddafb59c 100644
--- a/mypy/options.py
+++ b/mypy/options.py
@@ -216,6 +216,12 @@ def __init__(self) -> None:
         # supports globbing
         self.files: Optional[List[str]] = None
 
+        # A comma-separated list of packages for mypy to type check;
+        self.packages = None  # type: Optional[List[str]]
+
+        # A comma-separated list of modules for mypy to type check;
+        self.modules = None  # type: Optional[List[str]]
+
         # Write junit.xml to given file
         self.junit_xml: Optional[str] = None
 
diff --git a/test-data/unit/cmdline.test b/test-data/unit/cmdline.test
index 93eb893d3c00..7ea0ae3ff698 100644
--- a/test-data/unit/cmdline.test
+++ b/test-data/unit/cmdline.test
@@ -788,6 +788,59 @@ p/a.py:4: error: Argument 1 to "foo" has incompatible type "str"; expected "int"
 p/b/__init__.py:5: error: Argument 1 to "bar" has incompatible type "str"; expected "int"
 c.py:2: error: Argument 1 to "bar" has incompatible type "str"; expected "int"
 
+[case testModulesAndPackagesInIni]
+# cmd: mypy
+[file mypy.ini]
+\[mypy]
+modules=c
+packages=p.a,p.b
+[file p/__init__.py]
+[file p/a.py]
+def foo(x):
+    # type: (int) -> str
+    return "x"
+foo("wrong")
+[file p/b/__init__.py]
+from ..a import foo
+def bar(a):
+    # type: (int) -> str
+    return foo(a)
+bar("wrong")
+[file c.py]
+import p.b
+p.b.bar("wrong")
+[out]
+p/a.py:4: error: Argument 1 to "foo" has incompatible type "str"; expected "int"
+p/b/__init__.py:5: error: Argument 1 to "bar" has incompatible type "str"; expected "int"
+c.py:2: error: Argument 1 to "bar" has incompatible type "str"; expected "int"
+
+[case testModulesAndPackagesAndFilesInIni]
+# cmd: mypy
+[file mypy.ini]
+\[mypy]
+modules=c
+packages=p.a,p.b
+files=meh.py
+[out]
+May only specify one of: module/package or files. Ignoring key: files
+Can't find package 'p.a'
+== Return code: 2
+
+
+[case testModulesAndPackagesAndFilesInIniModLater]
+# cmd: mypy
+[file mypy.ini]
+\[mypy]
+files=meh.py
+modules=c
+packages=p.a,p.b
+[out]
+May only specify one of: module/package or files. Ignoring key: modules
+May only specify one of: module/package or files. Ignoring key: packages
+mypy: cannot read file 'meh.py': No such file or directory
+== Return code: 2
+
+
 [case testSrcPEP420Packages]
 # cmd: mypy -p anamespace --namespace-packages
 [file mypy.ini]
@@ -1271,7 +1324,6 @@ y = 0  # type: str
 [out]
 pkg.py:1: error: Incompatible types in assignment (expression has type "int", variable has type "str")
 
-
 [case testCmdlineModuleAndIniFiles]
 # cmd: mypy -m pkg
 [file mypy.ini]