diff --git a/dvc/repo/checkout.py b/dvc/repo/checkout.py
index 51c3dc5f7a5..36a89f945c1 100644
--- a/dvc/repo/checkout.py
+++ b/dvc/repo/checkout.py
@@ -30,35 +30,6 @@ def _remove_unused_links(repo):
     return ret
 
 
-def get_all_files_numbers(pairs):
-    return sum(stage.get_all_files_number(filter_info) for stage, filter_info in pairs)
-
-
-def _collect_pairs(
-    self: "Repo", targets, with_deps: bool, recursive: bool
-) -> Set["StageInfo"]:
-    from dvc.stage.exceptions import StageFileBadNameError, StageFileDoesNotExistError
-
-    pairs: Set["StageInfo"] = set()
-    for target in targets:
-        try:
-            pairs.update(
-                self.stage.collect_granular(
-                    target, with_deps=with_deps, recursive=recursive
-                )
-            )
-        except (
-            StageFileDoesNotExistError,
-            StageFileBadNameError,
-            NoOutputOrStageError,
-        ) as exc:
-            if not target:
-                raise
-            raise CheckoutErrorSuggestGit(target) from exc
-
-    return pairs
-
-
 @locked
 def checkout(
     self,
@@ -70,13 +41,17 @@ def checkout(
     allow_missing=False,
     **kwargs,
 ):
+    from dvc import prompt
     from dvc.fs.callbacks import Callback
+    from dvc.repo.index import build_data_index
+    from dvc_data.index.checkout import ADD, DELETE, MODIFY
+    from dvc_data.index.checkout import checkout as icheckout
+    from dvc_data.index.diff import diff as idiff
 
     stats: Dict[str, List[str]] = {
         "added": [],
         "deleted": [],
         "modified": [],
-        "failed": [],
     }
     if not targets:
         targets = [None]
@@ -85,28 +60,64 @@ def checkout(
     if isinstance(targets, str):
         targets = [targets]
 
-    pairs = _collect_pairs(self, targets, with_deps, recursive)
-    total = get_all_files_numbers(pairs)
+    view = self.index.targets_view(
+        targets,
+        recursive=recursive,
+        with_deps=True,
+    )
+
+    old = build_data_index(view, self.root_dir, self.fs, compute_hash=True)
+
+    new = view.data["repo"]
+    #    failed = [entry for _, entry in new.iteritems() if not entry.hash_info and not (entry.meta and entry.meta.isdir)]
+
+    total = len(new)
     with Callback.as_tqdm_callback(
         unit="file",
         desc="Checkout",
         disable=total == 0,
     ) as cb:
-        cb.set_size(total)
-        for stage, filter_info in pairs:
-            result = stage.checkout(
-                force=force,
-                progress_callback=cb,
-                relink=relink,
-                filter_info=filter_info,
-                allow_missing=allow_missing,
-                **kwargs,
-            )
-            for key, items in result.items():
-                stats[key].extend(_fspath_dir(path) for path in items)
-
-    if stats.get("failed"):
-        raise CheckoutError(stats["failed"], stats)
-
-    del stats["failed"]
+        changes = icheckout(
+            new,
+            self.root_dir,
+            self.fs,
+            old=old,
+            callback=cb,
+            hash_only=True,
+            delete=True,
+            prompt=prompt.confirm,
+            update_meta=False,  # FIXME should be off by defeault
+            relink=relink,
+            **kwargs,
+        )
+
+    def _adapt_path(entry):
+        parts = list(entry.key)
+        if entry.meta and entry.meta.isdir:
+            parts.append("")
+        return self.fs.path.join(*parts)
+
+    stats["added"].extend(_adapt_path(change.new) for change in changes[ADD])
+    stats["deleted"].extend(_adapt_path(change.old) for change in changes[DELETE])
+    stats["modified"].extend(_adapt_path(change.new) for change in changes[MODIFY])
+
+    from itertools import chain
+
+    top_keys = {key for key, _ in new.iteritems(shallow=True)}
+    changed_keys = {
+        change.key for change in chain(changes[ADD], changes[DELETE], changes[MODIFY])
+    }
+    for key in top_keys:
+        for changed_key in changed_keys:
+            if len(changed_key) >= len(key) and changed_key[: len(key)] == key:
+                self.state.save_link(self.fs.path.join(self.root_dir, *key), self.fs)
+
+    failed = [
+        entry
+        for _, entry in new.iteritems()
+        if not entry.hash_info and not (entry.meta and entry.meta.isdir)
+    ]
+    if failed:
+        raise CheckoutError([_adapt_path(entry) for entry in failed], stats)
+
     return stats
diff --git a/dvc/repo/index.py b/dvc/repo/index.py
index 1a3227c991c..dbf89d0bd33 100644
--- a/dvc/repo/index.py
+++ b/dvc/repo/index.py
@@ -534,6 +534,8 @@ def _data_prefixes(self) -> Dict[str, "_DataPrefixes"]:
             lambda: _DataPrefixes(set(), set())
         )
         for out, filter_info in self._filtered_outs:
+            if not out.use_cache:
+                continue
             workspace, key = out.index_key
             if filter_info and out.fs.path.isin(filter_info, out.fs_path):
                 key = key + out.fs.path.relparts(filter_info, out.fs_path)
@@ -550,6 +552,9 @@ def data_keys(self) -> Dict[str, Set["DataIndexKey"]]:
         ret: Dict[str, Set["DataIndexKey"]] = defaultdict(set)
 
         for out, filter_info in self._filtered_outs:
+            if not out.use_cache:
+                continue
+
             workspace, key = out.index_key
             if filter_info and out.fs.path.isin(filter_info, out.fs_path):
                 key = key + out.fs.path.relparts(filter_info, out.fs_path)
diff --git a/tests/func/test_checkout.py b/tests/func/test_checkout.py
index d308b633fc3..012caa99577 100644
--- a/tests/func/test_checkout.py
+++ b/tests/func/test_checkout.py
@@ -463,7 +463,13 @@ def test_stats_on_checkout(tmp_dir, dvc, scm):
 
     scm.checkout("-")
     stats = dvc.checkout()
-    assert set(stats["added"]) == {"bar", "dir" + os.sep, "foo"}
+    assert set(stats["added"]) == {
+        "bar",
+        "dir" + os.sep,
+        os.path.join("dir", "subdir", "file"),
+        os.path.join("dir", "other"),
+        "foo",
+    }
 
     tmp_dir.gen({"lorem": "lorem", "bar": "new bar", "dir2": {"file": "file"}})
     (tmp_dir / "foo").unlink()
@@ -479,7 +485,11 @@ def test_stats_on_checkout(tmp_dir, dvc, scm):
     scm.checkout("-")
     stats = dvc.checkout()
     assert set(stats["modified"]) == {"bar"}
-    assert set(stats["added"]) == {"dir2" + os.sep, "lorem"}
+    assert set(stats["added"]) == {
+        "dir2" + os.sep,
+        os.path.join("dir2", "file"),
+        "lorem",
+    }
     assert set(stats["deleted"]) == {"foo"}