diff --git a/pym/gentoolkit/eclean/clean.py b/pym/gentoolkit/eclean/clean.py
index 87d7aaca..1d4f4c20 100644
--- a/pym/gentoolkit/eclean/clean.py
+++ b/pym/gentoolkit/eclean/clean.py
@@ -5,6 +5,7 @@
 
 
 import os
+import shutil
 import sys
 
 import gentoolkit.pprinter as pp
@@ -23,7 +24,7 @@ def __init__(self, controller, quiet):
         self.controller = controller
         self.quiet = quiet
 
-    def clean_dist(self, clean_dict):
+    def clean_dist(self, clean_dict, git):
         """Calculate size of each entry for display, prompt user if needed,
         delete files if approved and return the total size of files that
         have been deleted.
@@ -39,6 +40,7 @@ def clean_dist(self, clean_dict):
         for key in sorted(clean_dict):
             clean_size += self._clean_files(clean_dict[key], key, file_type)
         # return total size of deleted or to delete files
+        clean_size += self._clean_git_src(git)
         return clean_size
 
     def clean_pkgs(self, clean_dict, pkgdir):
@@ -69,7 +71,7 @@ def clean_pkgs(self, clean_dict, pkgdir):
         # return total size of deleted or to delete files
         return clean_size
 
-    def pretend_clean(self, clean_dict):
+    def pretend_clean(self, clean_dict, git={}):
         """Shortcut function that calculates total space savings
         for the files in clean_dict.
 
@@ -80,6 +82,8 @@ def pretend_clean(self, clean_dict):
         file_type = "file"
         clean_size = 0
         # tally all entries one by one; sorting helps reading
+        if git:
+            clean_size += self._clean_git_src(git, pretend=True)
         for key in sorted(clean_dict):
             key_size = self._get_size(clean_dict[key])
             self.controller(key_size, key, clean_dict[key], file_type)
@@ -148,3 +152,30 @@ def _clean_files(self, files, key, file_type):
                     print(pp.error("Could not delete " + file_), file=sys.stderr)
                     print(pp.error("Error: %s" % str(er)), file=sys.stderr)
         return clean_size
+
+    def _clean_git_src(self, deprecated_git, pretend=False):
+        clean_size = 0
+        for checkout in deprecated_git:
+            csize = 0
+            for path, dirs, files in os.walk(checkout):
+                for f in files:
+                    fp = os.path.join(path, f)
+                    try:
+                        statinfo = os.stat(fp)
+                    except OSError as er:
+                        print(
+                            pp.error("Could not get stat info for:" + fp),
+                            file=sys.stderr,
+                        )
+                        print(pp.error("Error: %s" % str(er)), file=sys.stderr)
+                    clean_size += statinfo.st_size
+                    csize += statinfo.st_size
+
+            try:
+                self.controller(csize, checkout, checkout, "checkout")
+                if not pretend:
+                    shutil.rmtree(checkout)
+            except OSError as er:
+                print(pp.error("Could not delete " + checkout), file=sys.stderr)
+                print(pp.error("Error: %s" % str(er)), file=sys.stderr)
+        return clean_size
diff --git a/pym/gentoolkit/eclean/cli.py b/pym/gentoolkit/eclean/cli.py
index b180641b..a3120f58 100644
--- a/pym/gentoolkit/eclean/cli.py
+++ b/pym/gentoolkit/eclean/cli.py
@@ -13,25 +13,25 @@
 __productname__ = "eclean"
 __description__ = "A cleaning tool for Gentoo distfiles and binaries."
 
+import getopt
 import os
-import sys
 import re
+import sys
 import time
-import getopt
 
 import portage
-from portage.output import white, yellow, turquoise, green, red
+from portage.output import green, red, turquoise, white, yellow
 
 import gentoolkit.pprinter as pp
+from gentoolkit.eclean.clean import CleanUp
+from gentoolkit.eclean.exclude import ParseExcludeFileException, parseExcludeFile
+from gentoolkit.eclean.output import OutputControl
 from gentoolkit.eclean.search import (
     DistfilesSearch,
     findPackages,
-    port_settings,
     pkgdir,
+    port_settings,
 )
-from gentoolkit.eclean.exclude import parseExcludeFile, ParseExcludeFileException
-from gentoolkit.eclean.clean import CleanUp
-from gentoolkit.eclean.output import OutputControl
 
 # from gentoolkit.eclean.dbapi import Dbapi
 from gentoolkit.eprefix import EPREFIX
@@ -309,6 +309,10 @@ def printUsage(_error=None, help=None, unresolved_invalids=None):
             "   " + '"two hundreds kilobytes", etc.  Units are: ' + "G, M, K and B.",
             file=out,
         )
+        print(
+            yellow(" --skip-git") + "  - skip cleaning of git3_src ",
+            file=out,
+        )
         print(file=out)
     print(
         "More detailed instruction can be found in",
@@ -420,6 +424,8 @@ def optionSwitch(option, opts, action=None):
                 options["unique-use"] = True
             elif o in ("--no-clean-invalid"):
                 options["no-clean-invalid"] = True
+            elif o in ("--skip-git"):
+                options["skip-git"] = True
             else:
                 return_code = False
         # sanity check of --deep only options:
@@ -457,7 +463,11 @@ def optionSwitch(option, opts, action=None):
         "verbose",
     ]
     getopt_options["short"]["distfiles"] = "fs:"
-    getopt_options["long"]["distfiles"] = ["fetch-restricted", "size-limit="]
+    getopt_options["long"]["distfiles"] = [
+        "fetch-restricted",
+        "size-limit=",
+        "skip-git",
+    ]
     getopt_options["short"]["packages"] = "iu"
     getopt_options["long"]["packages"] = [
         "ignore-failure",
@@ -481,6 +491,7 @@ def optionSwitch(option, opts, action=None):
     options["ignore-failure"] = False
     options["no-clean-invalid"] = False
     options["unique-use"] = False
+    options["skip-git"] = False
     # if called by a well-named symlink, set the action accordingly:
     action = None
     # temp print line to ensure it is the svn/branch code running, etc..
@@ -546,6 +557,7 @@ def doAction(action, options, exclude={}, output=None):
         files_type = "distfiles"
     saved = {}
     deprecated = {}
+    git = []
     # find files to delete, depending on the action
     if not options["quiet"]:
         output.einfo("Building file list for " + action + " cleaning...")
@@ -567,7 +579,7 @@ def doAction(action, options, exclude={}, output=None):
             # portdb=Dbapi(portage.db[portage.root]["porttree"].dbapi),
             # var_dbapi=Dbapi(portage.db[portage.root]["vartree"].dbapi),
         )
-        clean_me, saved, deprecated = engine.findDistfiles(
+        clean_me, saved, deprecated, git = engine.findDistfiles(
             exclude=exclude,
             destructive=options["destructive"],
             fetch_restricted=options["fetch-restricted"],
@@ -581,7 +593,7 @@ def doAction(action, options, exclude={}, output=None):
     cleaner = CleanUp(output.progress_controller, options["quiet"])
 
     # actually clean files if something was found
-    if clean_me:
+    if clean_me or git:
         # verbose pretend message
         if options["pretend"] and not options["quiet"]:
             output.einfo("Here are the " + files_type + " that would be deleted:")
@@ -590,9 +602,13 @@ def doAction(action, options, exclude={}, output=None):
             output.einfo("Cleaning " + files_type + "...")
         # do the cleanup, and get size of deleted files
         if options["pretend"]:
-            clean_size = cleaner.pretend_clean(clean_me)
+            if options["skip-git"]:
+                git = {}
+            clean_size = cleaner.pretend_clean(clean_me, git)
         elif action in ["distfiles"]:
-            clean_size = cleaner.clean_dist(clean_me)
+            if options["skip-git"]:
+                git = {}
+            clean_size = cleaner.clean_dist(clean_me, git)
         elif action in ["packages"]:
             clean_size = cleaner.clean_pkgs(clean_me, pkgdir)
         # vocabulary for final message
@@ -602,7 +618,7 @@ def doAction(action, options, exclude={}, output=None):
             verb = "were"
         # display freed space
         if not options["quiet"]:
-            output.total("normal", clean_size, len(clean_me), verb, action)
+            output.total("normal", clean_size, len(clean_me) + len(git), verb, action)
     # nothing was found
     elif not options["quiet"]:
         output.einfo("Your " + action + " directory was already clean.")
diff --git a/pym/gentoolkit/eclean/output.py b/pym/gentoolkit/eclean/output.py
index ebba499c..67387380 100644
--- a/pym/gentoolkit/eclean/output.py
+++ b/pym/gentoolkit/eclean/output.py
@@ -5,7 +5,9 @@
 
 
 import sys
-from portage.output import blue, yellow, teal, green, red
+
+from portage.output import blue, green, red, teal, yellow
+
 from gentoolkit.pprinter import cpv, number
 
 
diff --git a/pym/gentoolkit/eclean/search.py b/pym/gentoolkit/eclean/search.py
index a2ac0ce4..c01a6ba4 100644
--- a/pym/gentoolkit/eclean/search.py
+++ b/pym/gentoolkit/eclean/search.py
@@ -7,6 +7,7 @@
 import os
 import stat
 import sys
+import shlex
 from functools import partial
 from typing import Optional
 
@@ -16,13 +17,12 @@
 
 import gentoolkit.pprinter as pp
 from gentoolkit.eclean.exclude import (
-    exclDictMatchCP,
     exclDictExpand,
     exclDictExpandPkgname,
+    exclDictMatchCP,
     exclMatchFilename,
 )
 
-
 # Misc. shortcuts to some portage stuff:
 port_settings = portage.settings
 pkgdir = port_settings["PKGDIR"]
@@ -134,6 +134,7 @@ def findDistfiles(
         # gather the files to be cleaned
         self.output("...checking limits for %d ebuild sources" % len(pkgs))
 
+        git = self.git_check(_distdir)
         checks = self._get_default_checks(size_limit, time_limit, exclude, destructive)
         checks.extend(extra_checks)
         clean_me = self._check_limits(_distdir, checks, clean_me)
@@ -148,7 +149,7 @@ def findDistfiles(
                 + "%s remaining candidates to clean" % len(clean_me)
             )
             clean_me, saved = self._check_excludes(exclude, clean_me)
-        return clean_me, saved, deprecated
+        return clean_me, saved, deprecated, git
 
     # begin _check_limits code block
 
@@ -332,6 +333,31 @@ def _non_destructive(
             deprecated.update(_deprecated)
         return pkgs, deprecated
 
+    def git_check(self, distdir):
+        """Checks $DISTDIR/git3-src for checkouts which are not in the vardb"""
+        git_src = os.path.join(distdir, "git3-src")
+        expected_dirs = set()
+        for i in set(self.vardb.cpv_all()):
+            if "live" in self.vardb.aux_get(i, ["PROPERTIES"]):
+                try:
+                    # try to get the dir names of the cloned
+                    # repos from the environment file.
+                    vcs_dir = {
+                        i.split("=")[-1].strip('"')
+                        for i in (
+                            shlex.split(
+                                self.vardb._aux_env_search(i, ["EVCS_STORE_DIRS"])[
+                                    "EVCS_STORE_DIRS"
+                                ].strip("()")
+                            )
+                        )
+                    }
+                    expected_dirs.update(vcs_dir)
+                except KeyError:
+                    pass
+        actual_dirs = {os.path.join(git_src, i) for i in os.listdir(git_src)}
+        return actual_dirs.difference(expected_dirs)
+
     def _fetch_restricted(self, pkgs_, cpvs):
         """perform fetch restricted non-destructive source
         filename lookups