diff --git a/src/plugins/clangtools/clangtidyclazytool.cpp b/src/plugins/clangtools/clangtidyclazytool.cpp
index eb4964d5fe8..b1afe494e08 100644
--- a/src/plugins/clangtools/clangtidyclazytool.cpp
+++ b/src/plugins/clangtools/clangtidyclazytool.cpp
@@ -407,7 +407,7 @@ void ClangTidyClazyTool::updateRunActions()
         m_startAction->setToolTip(toolTip);
         m_startAction->setEnabled(canRun);
         m_stopAction->setEnabled(false);
-        m_clear->setEnabled(m_diagnosticModel->diagnosticsCount());
+        m_clear->setEnabled(m_diagnosticModel->diagnostics().count());
     }
 }
 
@@ -418,7 +418,7 @@ void ClangTidyClazyTool::handleStateUpdate()
     QTC_ASSERT(m_diagnosticModel, return);
     QTC_ASSERT(m_diagnosticFilterModel, return);
 
-    const int issuesFound = m_diagnosticModel->diagnosticsCount();
+    const int issuesFound = m_diagnosticModel->diagnostics().count();
     const int issuesVisible = m_diagnosticFilterModel->rowCount();
     m_goBack->setEnabled(issuesVisible > 1);
     m_goNext->setEnabled(issuesVisible > 1);
@@ -439,10 +439,11 @@ void ClangTidyClazyTool::handleStateUpdate()
 }
 
 QList<Diagnostic> ClangTidyClazyTool::read(const QString &filePath,
+                                           const Utils::FileName &projectRootDir,
                                            const QString &logFilePath,
                                            QString *errorMessage) const
 {
-    return readSerializedDiagnostics(filePath, logFilePath, errorMessage);
+    return readSerializedDiagnostics(filePath, projectRootDir, logFilePath, errorMessage);
 }
 
 } // namespace Internal
diff --git a/src/plugins/clangtools/clangtidyclazytool.h b/src/plugins/clangtools/clangtidyclazytool.h
index 48ffe07906f..a82ff809993 100644
--- a/src/plugins/clangtools/clangtidyclazytool.h
+++ b/src/plugins/clangtools/clangtidyclazytool.h
@@ -54,6 +54,7 @@ public:
     void startTool(bool askUserForFileSelection) final;
 
     QList<Diagnostic> read(const QString &filePath,
+                           const Utils::FileName &projectRootDir,
                            const QString &logFilePath,
                            QString *errorMessage) const final;
 
diff --git a/src/plugins/clangtools/clangtool.cpp b/src/plugins/clangtools/clangtool.cpp
index 8ca03b9634b..b02868cb5dc 100644
--- a/src/plugins/clangtools/clangtool.cpp
+++ b/src/plugins/clangtools/clangtool.cpp
@@ -135,7 +135,7 @@ void ClangTool::initDiagnosticView()
     m_diagnosticView->setAutoScroll(false);
 }
 
-QList<Diagnostic> ClangTool::diagnostics() const
+QSet<Diagnostic> ClangTool::diagnostics() const
 {
     return m_diagnosticModel->diagnostics();
 }
diff --git a/src/plugins/clangtools/clangtool.h b/src/plugins/clangtools/clangtool.h
index 93f7a610505..de4d08ceb9d 100644
--- a/src/plugins/clangtools/clangtool.h
+++ b/src/plugins/clangtools/clangtool.h
@@ -31,6 +31,7 @@
 #include <cpptools/projectinfo.h>
 
 namespace Debugger { class DetailedErrorView; }
+namespace Utils { class FileName; }
 
 namespace ClangTools {
 namespace Internal {
@@ -49,6 +50,7 @@ public:
     virtual void startTool(bool askUserForFileSelection) = 0;
 
     virtual QList<Diagnostic> read(const QString &filePath,
+                                   const Utils::FileName &projectRootDir,
                                    const QString &logFilePath,
                                    QString *errorMessage) const = 0;
 
@@ -56,7 +58,7 @@ public:
                                bool askUserForFileSelection) const;
 
     // For testing.
-    QList<Diagnostic> diagnostics() const;
+    QSet<Diagnostic> diagnostics() const;
 
     const QString &name() const;
 
diff --git a/src/plugins/clangtools/clangtoolruncontrol.cpp b/src/plugins/clangtools/clangtoolruncontrol.cpp
index 8a379095d93..a25d3fc9103 100644
--- a/src/plugins/clangtools/clangtoolruncontrol.cpp
+++ b/src/plugins/clangtools/clangtoolruncontrol.cpp
@@ -387,13 +387,24 @@ void ClangToolRunControl::analyzeNextFile()
                   Utils::StdOutFormat);
 }
 
+static Utils::FileName cleanPath(const Utils::FileName &filePath)
+{
+    return Utils::FileName::fromString(QDir::cleanPath(filePath.toString()));
+}
+
 void ClangToolRunControl::onRunnerFinishedWithSuccess(const QString &filePath)
 {
     const QString logFilePath = qobject_cast<ClangToolRunner *>(sender())->logFilePath();
     qCDebug(LOG) << "onRunnerFinishedWithSuccess:" << logFilePath;
 
+    QTC_ASSERT(m_projectInfo.project(), return);
+    const Utils::FileName projectRootDir = cleanPath(m_projectInfo.project()->projectDirectory());
+
     QString errorMessage;
-    const QList<Diagnostic> diagnostics = tool()->read(filePath, logFilePath, &errorMessage);
+    const QList<Diagnostic> diagnostics = tool()->read(filePath,
+                                                       projectRootDir,
+                                                       logFilePath,
+                                                       &errorMessage);
     QFile::remove(logFilePath); // Clean-up.
 
     if (!errorMessage.isEmpty()) {
diff --git a/src/plugins/clangtools/clangtoolsdiagnostic.cpp b/src/plugins/clangtools/clangtoolsdiagnostic.cpp
index 4f04c03338f..cb1f4ead62c 100644
--- a/src/plugins/clangtools/clangtoolsdiagnostic.cpp
+++ b/src/plugins/clangtools/clangtoolsdiagnostic.cpp
@@ -38,5 +38,13 @@ bool Diagnostic::isValid() const
     return !description.isEmpty();
 }
 
+quint32 qHash(const Diagnostic &diagnostic)
+{
+    return qHash(diagnostic.description)
+         ^ qHash(diagnostic.location.filePath)
+         ^ diagnostic.location.line
+         ^ diagnostic.location.column;
+}
+
 } // namespace Internal
 } // namespace ClangTools
diff --git a/src/plugins/clangtools/clangtoolsdiagnostic.h b/src/plugins/clangtools/clangtoolsdiagnostic.h
index 9f6b5a99690..eb16803638f 100644
--- a/src/plugins/clangtools/clangtoolsdiagnostic.h
+++ b/src/plugins/clangtools/clangtoolsdiagnostic.h
@@ -66,6 +66,8 @@ public:
     bool hasFixits = false;
 };
 
+quint32 qHash(const Diagnostic &diagnostic);
+
 } // namespace Internal
 } // namespace ClangTools
 
diff --git a/src/plugins/clangtools/clangtoolsdiagnosticmodel.cpp b/src/plugins/clangtools/clangtoolsdiagnosticmodel.cpp
index eb13577b54b..4de6f8dcc6c 100644
--- a/src/plugins/clangtools/clangtoolsdiagnosticmodel.cpp
+++ b/src/plugins/clangtools/clangtoolsdiagnosticmodel.cpp
@@ -35,9 +35,12 @@
 #include <utils/utilsicons.h>
 
 #include <QFileInfo>
+#include <QLoggingCategory>
 
 #include <cmath>
 
+static Q_LOGGING_CATEGORY(LOG, "qtc.clangtools.model", QtWarningMsg)
+
 namespace ClangTools {
 namespace Internal {
 
@@ -60,6 +63,19 @@ ClangToolsDiagnosticModel::ClangToolsDiagnosticModel(QObject *parent)
     connectFileWatcher();
 }
 
+QDebug operator<<(QDebug debug, const Diagnostic &d)
+{
+    return debug << "category:" << d.category
+                 << "type:" << d.type
+                 << "context:" << d.issueContext
+                 << "contextKind:" << d.issueContextKind
+                 << "hasFixits:" << d.hasFixits
+                 << "explainingSteps:" << d.explainingSteps.size()
+                 << "location:" << d.location
+                 << "description:" << d.description
+                 ;
+}
+
 void ClangToolsDiagnosticModel::addDiagnostics(const QList<Diagnostic> &diagnostics)
 {
     const auto onFixitStatusChanged = [this](FixitStatus newStatus) {
@@ -70,28 +86,28 @@ void ClangToolsDiagnosticModel::addDiagnostics(const QList<Diagnostic> &diagnost
         emit fixItsToApplyCountChanged(m_fixItsToApplyCount);
     };
 
-    if (!diagnostics.empty())
-        addWatchedPath(diagnostics.front().location.filePath);
+    for (const Diagnostic &d : diagnostics) {
+        const int previousItemCount = m_diagnostics.count();
+        m_diagnostics.insert(d);
+        if (m_diagnostics.count() == previousItemCount) {
+            qCDebug(LOG) << "Not adding duplicate diagnostic:" << d;
+            continue;
+        }
 
-    for (const Diagnostic &d : diagnostics)
+        qCDebug(LOG) << "Adding diagnostic:" << d;
+        addWatchedPath(d.location.filePath);
         rootItem()->appendChild(new DiagnosticItem(d, onFixitStatusChanged, this));
+    }
 }
 
-QList<Diagnostic> ClangToolsDiagnosticModel::diagnostics() const
+QSet<Diagnostic> ClangToolsDiagnosticModel::diagnostics() const
 {
-    QList<Diagnostic> diags;
-    for (const Utils::TreeItem * const item : *rootItem())
-        diags << static_cast<const DiagnosticItem *>(item)->diagnostic();
-    return diags;
-}
-
-int ClangToolsDiagnosticModel::diagnosticsCount() const
-{
-    return rootItem()->childCount();
+    return m_diagnostics;
 }
 
 void ClangToolsDiagnosticModel::clear()
 {
+    m_diagnostics.clear();
     clearAndSetupCache();
     Utils::TreeModel<>::clear();
 }
diff --git a/src/plugins/clangtools/clangtoolsdiagnosticmodel.h b/src/plugins/clangtools/clangtoolsdiagnosticmodel.h
index 8ad10ca5ac0..b877b93b867 100644
--- a/src/plugins/clangtools/clangtoolsdiagnosticmodel.h
+++ b/src/plugins/clangtools/clangtoolsdiagnosticmodel.h
@@ -98,10 +98,8 @@ class ClangToolsDiagnosticModel : public Utils::TreeModel<>
 public:
     ClangToolsDiagnosticModel(QObject *parent = nullptr);
 
-    virtual void addDiagnostics(const QList<Diagnostic> &diagnostics);
-    virtual QList<Diagnostic> diagnostics() const;
-
-    int diagnosticsCount() const;
+    void addDiagnostics(const QList<Diagnostic> &diagnostics);
+    QSet<Diagnostic> diagnostics() const;
 
     enum ItemRole {
         DiagnosticRole = Debugger::DetailedErrorView::FullTextRole + 1
@@ -121,6 +119,7 @@ private:
     void clearAndSetupCache();
 
 private:
+    QSet<Diagnostic> m_diagnostics;
     std::map<QVector<ExplainingStep>, QVector<DiagnosticItem *>> stepsToItemsCache;
     std::unique_ptr<QFileSystemWatcher> m_filesWatcher;
     int m_fixItsToApplyCount = 0;
diff --git a/src/plugins/clangtools/clangtoolslogfilereader.cpp b/src/plugins/clangtools/clangtoolslogfilereader.cpp
index d7602a26691..d1e98fac87b 100644
--- a/src/plugins/clangtools/clangtoolslogfilereader.cpp
+++ b/src/plugins/clangtools/clangtoolslogfilereader.cpp
@@ -59,6 +59,7 @@ static Debugger::DiagnosticLocation diagLocationFromSourceLocation(CXSourceLocat
 
     Debugger::DiagnosticLocation location;
     location.filePath = fromCXString(clang_getFileName(file));
+    location.filePath = QDir::cleanPath(location.filePath); // Normalize to find duplicates later
     location.line = line;
     location.column = column;
     return location;
@@ -118,7 +119,9 @@ static ExplainingStep buildFixIt(const CXDiagnostic cxDiagnostic, unsigned index
     return fixItStep;
 }
 
-static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic, const QString &nativeFilePath)
+static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic,
+                                  const Utils::FileName &projectRootDir,
+                                  const QString &nativeFilePath)
 {
     Diagnostic diagnostic;
     diagnostic.type = cxDiagnosticType(cxDiagnostic);
@@ -130,7 +133,13 @@ static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic, const QString
         return diagnostic;
 
     diagnostic.location = diagLocationFromSourceLocation(cxLocation);
-    if (diagnostic.location.filePath != nativeFilePath)
+    const auto diagnosticFilePath = Utils::FileName::fromString(diagnostic.location.filePath);
+    if (!diagnosticFilePath.isChildOf(projectRootDir))
+        return diagnostic;
+
+    // TODO: Introduce CppTools::ProjectFile::isGenerated to filter these out properly
+    const QString fileName = diagnosticFilePath.fileName();
+    if ((fileName.startsWith("ui_") && fileName.endsWith(".h")) || fileName.endsWith(".moc"))
         return diagnostic;
 
     CXDiagnosticSet cxChildDiagnostics = clang_getChildDiagnostics(cxDiagnostic);
@@ -165,6 +174,7 @@ static Diagnostic buildDiagnostic(const CXDiagnostic cxDiagnostic, const QString
 }
 
 static QList<Diagnostic> readSerializedDiagnostics_helper(const QString &filePath,
+                                                          const Utils::FileName &projectRootDir,
                                                           const QString &logFilePath)
 {
     QList<Diagnostic> list;
@@ -187,7 +197,7 @@ static QList<Diagnostic> readSerializedDiagnostics_helper(const QString &filePat
         Utils::ExecuteOnDestruction cleanUpDiagnostic([&]() {
             clang_disposeDiagnostic(cxDiagnostic);
         });
-        const Diagnostic diagnostic = buildDiagnostic(cxDiagnostic, nativeFilePath);
+        const Diagnostic diagnostic = buildDiagnostic(cxDiagnostic, projectRootDir, nativeFilePath);
         if (!diagnostic.isValid())
             continue;
 
@@ -213,13 +223,14 @@ static bool checkFilePath(const QString &filePath, QString *errorMessage)
 }
 
 QList<Diagnostic> readSerializedDiagnostics(const QString &filePath,
+                                            const Utils::FileName &projectRootDir,
                                             const QString &logFilePath,
                                             QString *errorMessage)
 {
     if (!checkFilePath(logFilePath, errorMessage))
         return QList<Diagnostic>();
 
-    return readSerializedDiagnostics_helper(filePath, logFilePath);
+    return readSerializedDiagnostics_helper(filePath, projectRootDir, logFilePath);
 }
 
 } // namespace Internal
diff --git a/src/plugins/clangtools/clangtoolslogfilereader.h b/src/plugins/clangtools/clangtoolslogfilereader.h
index 7118390935f..3d8a776932e 100644
--- a/src/plugins/clangtools/clangtoolslogfilereader.h
+++ b/src/plugins/clangtools/clangtoolslogfilereader.h
@@ -35,6 +35,7 @@ namespace ClangTools {
 namespace Internal {
 
 QList<Diagnostic> readSerializedDiagnostics(const QString &filePath,
+                                            const Utils::FileName &projectRootDir,
                                             const QString &logFilePath,
                                             QString *errorMessage);