diff --git a/python/python-psi-impl/src/com/jetbrains/python/codeInsight/completion/PyClassNameCompletionContributor.java b/python/python-psi-impl/src/com/jetbrains/python/codeInsight/completion/PyClassNameCompletionContributor.java
index 63ee2f36d55c..f17f1a435b4a 100644
--- a/python/python-psi-impl/src/com/jetbrains/python/codeInsight/completion/PyClassNameCompletionContributor.java
+++ b/python/python-psi-impl/src/com/jetbrains/python/codeInsight/completion/PyClassNameCompletionContributor.java
@@ -21,6 +21,7 @@ import com.intellij.psi.util.QualifiedName;
 import com.intellij.util.containers.ContainerUtil;
 import com.jetbrains.python.codeInsight.controlflow.ScopeOwner;
 import com.jetbrains.python.codeInsight.dataflow.scope.ScopeUtil;
+import com.jetbrains.python.codeInsight.userSkeletons.PyUserSkeletonsUtil;
 import com.jetbrains.python.psi.*;
 import com.jetbrains.python.psi.resolve.QualifiedNameFinder;
 import com.jetbrains.python.psi.search.PySearchUtilBase;
@@ -114,7 +115,8 @@ public class PyClassNameCompletionContributor extends PyExtendedCompletionContri
                                                                        @NotNull Class<T> elementClass,
                                                                        @NotNull Function<LookupElement, LookupElement> elementHandler) {
     final Project project = targetFile.getProject();
-    final GlobalSearchScope scope = PySearchUtilBase.excludeSdkTestsScope(targetFile);
+    final GlobalSearchScope scope = PySearchUtilBase.excludeSdkTestsScope(targetFile)
+      .intersectWith(GlobalSearchScope.notScope(PyUserSkeletonsUtil.getUserSkeletonsDirectoryScope(project)));
     final Set<String> alreadySuggested = new HashSet<>();
 
     StubIndex stubIndex = StubIndex.getInstance();
diff --git a/python/python-psi-impl/src/com/jetbrains/python/codeInsight/userSkeletons/PyUserSkeletonsUtil.java b/python/python-psi-impl/src/com/jetbrains/python/codeInsight/userSkeletons/PyUserSkeletonsUtil.java
index c5cbfcdf824c..4c27d9e18825 100644
--- a/python/python-psi-impl/src/com/jetbrains/python/codeInsight/userSkeletons/PyUserSkeletonsUtil.java
+++ b/python/python-psi-impl/src/com/jetbrains/python/codeInsight/userSkeletons/PyUserSkeletonsUtil.java
@@ -29,6 +29,8 @@ import com.intellij.psi.PsiDirectory;
 import com.intellij.psi.PsiElement;
 import com.intellij.psi.PsiFile;
 import com.intellij.psi.PsiManager;
+import com.intellij.psi.search.GlobalSearchScope;
+import com.intellij.psi.search.GlobalSearchScopesCore;
 import com.intellij.psi.util.QualifiedName;
 import com.intellij.util.containers.ContainerUtil;
 import com.jetbrains.python.PythonHelpersLocator;
@@ -115,6 +117,17 @@ public class PyUserSkeletonsUtil {
     return skeletonsDir != null && VfsUtilCore.isAncestor(skeletonsDir, virtualFile, false);
   }
 
+  @NotNull
+  public static GlobalSearchScope getUserSkeletonsDirectoryScope(@NotNull Project project) {
+    VirtualFile userSkeletonsDirectory = getUserSkeletonsDirectory();
+    if (userSkeletonsDirectory != null) {
+      return new GlobalSearchScopesCore.DirectoryScope(project, userSkeletonsDirectory, true);
+    }
+    else {
+      return GlobalSearchScope.EMPTY_SCOPE;
+    }
+  }
+
   public static boolean isStandardLibrarySkeleton(@NotNull VirtualFile virtualFile) {
     final VirtualFile skeletonsDir = getUserSkeletonsDirectory();
     if (skeletonsDir == null) {
diff --git a/python/python-psi-impl/src/com/jetbrains/python/psi/stubs/PyModuleNameIndex.java b/python/python-psi-impl/src/com/jetbrains/python/psi/stubs/PyModuleNameIndex.java
index 3afc605dea2a..0eea3886b58d 100644
--- a/python/python-psi-impl/src/com/jetbrains/python/psi/stubs/PyModuleNameIndex.java
+++ b/python/python-psi-impl/src/com/jetbrains/python/psi/stubs/PyModuleNameIndex.java
@@ -86,16 +86,16 @@ public class PyModuleNameIndex extends ScalarIndexExtension<String> {
   @NotNull
   public static List<PyFile> find(@NotNull String name, @NotNull Project project, boolean includeNonProjectItems) {
     final List<PyFile> results = new ArrayList<>();
-    final GlobalSearchScope scope = includeNonProjectItems
+    final GlobalSearchScope baseScope = includeNonProjectItems
                                     ? PySearchUtilBase.excludeSdkTestsScope(project)
                                     : GlobalSearchScope.projectScope(project);
+    final GlobalSearchScope scope = baseScope
+      .intersectWith(GlobalSearchScope.notScope(PyUserSkeletonsUtil.getUserSkeletonsDirectoryScope(project)));
     final Collection<VirtualFile> files = FileBasedIndex.getInstance().getContainingFiles(NAME, name, scope);
     for (VirtualFile virtualFile : files) {
       final PsiFile psiFile = PsiManager.getInstance(project).findFile(virtualFile);
       if (psiFile instanceof PyFile) {
-        if (!PyUserSkeletonsUtil.isUnderUserSkeletonsDirectory(psiFile)) {
-          results.add((PyFile)psiFile);
-        }
+        results.add((PyFile)psiFile);
       }
     }
     return results;
diff --git a/python/testData/completion/className/pythonSkeletonsVariantsNotSuggested/pythonSkeletonsVariantsNotSuggested.py b/python/testData/completion/className/pythonSkeletonsVariantsNotSuggested/pythonSkeletonsVariantsNotSuggested.py
new file mode 100644
index 000000000000..eb7e25cb8d1a
--- /dev/null
+++ b/python/testData/completion/className/pythonSkeletonsVariantsNotSuggested/pythonSkeletonsVariantsNotSuggested.py
@@ -0,0 +1 @@
+nd<caret>
diff --git a/python/testSrc/com/jetbrains/python/PyClassNameCompletionTest.java b/python/testSrc/com/jetbrains/python/PyClassNameCompletionTest.java
index 2ee54383f31e..221fe1022f96 100644
--- a/python/testSrc/com/jetbrains/python/PyClassNameCompletionTest.java
+++ b/python/testSrc/com/jetbrains/python/PyClassNameCompletionTest.java
@@ -11,10 +11,13 @@ import com.intellij.psi.codeStyle.CommonCodeStyleSettings;
 import com.intellij.testFramework.fixtures.TestLookupElementPresentation;
 import com.intellij.util.containers.ContainerUtil;
 import com.jetbrains.python.codeInsight.PyCodeInsightSettings;
+import com.jetbrains.python.codeInsight.userSkeletons.PyUserSkeletonsUtil;
 import com.jetbrains.python.fixtures.PyTestCase;
 import com.jetbrains.python.formatter.PyCodeStyleSettings;
+import com.jetbrains.python.psi.PyClass;
 import com.jetbrains.python.psi.PyQualifiedNameOwner;
 import com.jetbrains.python.psi.resolve.QualifiedNameFinder;
+import com.jetbrains.python.psi.stubs.PyClassNameIndex;
 import one.util.streamex.StreamEx;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -180,6 +183,18 @@ public class PyClassNameCompletionTest extends PyTestCase {
     assertEquals(" (pkg.mod)", varPresentation.getTailText());
   }
 
+  // PY-45566
+  public void testPythonSkeletonsVariantsNotSuggested() {
+    LookupElement[] lookupElements = doExtendedCompletion();
+
+    LookupElement ndarray = ContainerUtil.find(lookupElements, variant -> variant.getLookupString().equals("ndarray"));
+    assertNull(ndarray);
+
+    PyClass ndarrayUserSkeleton = PyClassNameIndex.findClass("numpy.core.multiarray.ndarray", myFixture.getProject());
+    assertNotNull(ndarrayUserSkeleton);
+    assertTrue(PyUserSkeletonsUtil.isUnderUserSkeletonsDirectory(ndarrayUserSkeleton.getContainingFile()));
+  }
+
   private void doTest() {
     LookupElement[] lookupElements = doExtendedCompletion();
     if (lookupElements != null) {