diff --git a/src/vs/workbench/api/node/extHostDiagnostics.ts b/src/vs/workbench/api/node/extHostDiagnostics.ts
index 0fa5eeaa480..38b7850a6c6 100644
--- a/src/vs/workbench/api/node/extHostDiagnostics.ts
+++ b/src/vs/workbench/api/node/extHostDiagnostics.ts
@@ -8,6 +8,7 @@ import {localize} from 'vs/nls';
 import {IThreadService} from 'vs/workbench/services/thread/common/threadService';
 import {IMarkerData} from 'vs/platform/markers/common/markers';
 import URI from 'vs/base/common/uri';
+import {compare} from 'vs/base/common/strings';
 import Severity from 'vs/base/common/severity';
 import * as vscode from 'vscode';
 import {MainContext, MainThreadDiagnosticsShape, ExtHostDiagnosticsShape} from './extHost.protocol';
@@ -72,20 +73,23 @@ export class DiagnosticCollection implements vscode.DiagnosticCollection {
 		} else if (Array.isArray(first)) {
 			// update many rows
 			toSync = [];
-			for (let entry of first) {
-				let [uri, diagnostics] = entry;
-				toSync.push(uri);
+			let lastUri: vscode.Uri;
+			for (const entry of first.slice(0).sort(DiagnosticCollection._compareTuplesByUri)) {
+				const [uri, diagnostics] = entry;
+				if (!lastUri || uri.toString() !== lastUri.toString()) {
+					if (lastUri && this._data[lastUri.toString()].length === 0) {
+						delete this._data[lastUri.toString()];
+					}
+					lastUri = uri;
+					toSync.push(uri);
+					this._data[uri.toString()] = [];
+				}
+
 				if (!diagnostics) {
 					// [Uri, undefined] means clear this
-					delete this._data[uri.toString()];
+					this._data[uri.toString()].length = 0;
 				} else {
-					// set or merge diagnostics
-					let existing = this._data[uri.toString()];
-					if (existing) {
-						existing.push(...diagnostics);
-					} else {
-						this._data[uri.toString()] = diagnostics;
-					}
+					this._data[uri.toString()].push(...diagnostics);
 				}
 			}
 		}
@@ -196,6 +200,10 @@ export class DiagnosticCollection implements vscode.DiagnosticCollection {
 			default: return Severity.Error;
 		}
 	}
+
+	private static _compareTuplesByUri(a: [vscode.Uri, vscode.Diagnostic[]], b: [vscode.Uri, vscode.Diagnostic[]]): number {
+		return compare(a[0].toString(), b[0].toString());
+	}
 }
 
 export class ExtHostDiagnostics extends ExtHostDiagnosticsShape {
diff --git a/src/vs/workbench/test/node/api/extHostDiagnostics.test.ts b/src/vs/workbench/test/node/api/extHostDiagnostics.test.ts
index 999f59de499..ec1c67b84ab 100644
--- a/src/vs/workbench/test/node/api/extHostDiagnostics.test.ts
+++ b/src/vs/workbench/test/node/api/extHostDiagnostics.test.ts
@@ -159,6 +159,35 @@ suite('ExtHostDiagnostics', () => {
 		collection.dispose();
 	});
 
+	test('diagnostics collection, set tuple overrides, #11547', function () {
+
+		let lastEntries: [URI, IMarkerData[]][];
+		let collection = new DiagnosticCollection('test', new class extends DiagnosticsShape {
+			$changeMany(owner: string, entries: [URI, IMarkerData[]][]): TPromise<any> {
+				lastEntries = entries;
+				return super.$changeMany(owner, entries);
+			}
+		});
+		let uri = URI.parse('sc:hightower');
+
+		collection.set([[uri, [new Diagnostic(new Range(0, 0, 1, 1), 'error')]]]);
+		assert.equal(collection.get(uri).length, 1);
+		assert.equal(collection.get(uri)[0].message, 'error');
+		assert.equal(lastEntries.length, 1);
+		let [[, data1]] = lastEntries;
+		assert.equal(data1.length, 1);
+		assert.equal(data1[0].message, 'error');
+		lastEntries = undefined;
+
+		collection.set([[uri, [new Diagnostic(new Range(0, 0, 1, 1), 'warning')]]]);
+		assert.equal(collection.get(uri).length, 1);
+		assert.equal(collection.get(uri)[0].message, 'warning');
+		assert.equal(lastEntries.length, 1);
+		let [[, data2]] = lastEntries;
+		assert.equal(data2.length, 1);
+		assert.equal(data2[0].message, 'warning');
+		lastEntries = undefined;
+	});
 
 	test('diagnostic capping', function () {