diff --git a/packages/ts-transformers/src/core/ct-helpers.ts b/packages/ts-transformers/src/core/ct-helpers.ts
index eff061d62..3f21b920f 100644
--- a/packages/ts-transformers/src/core/ct-helpers.ts
+++ b/packages/ts-transformers/src/core/ct-helpers.ts
@@ -79,13 +79,8 @@ export class CTHelpers {
 export function transformCtDirective(
   source: string,
 ): string {
-  // Throw when this symbol name is already in use
-  // for some reason.
-  if (source.indexOf(CT_HELPERS_IDENTIFIER) !== -1) {
-    throw new Error(
-      `Source cannot contain reserved '${CT_HELPERS_IDENTIFIER}' symbol.`,
-    );
-  }
+  checkCTHelperVar(source);
+
   const lines = source.split("\n");
   if (!lines[0] || !isCTSEnabled(lines[0])) {
     return source;
@@ -101,6 +96,27 @@ function isCTSEnabled(line: string) {
   return /^\/\/\/\s*<cts-enable\s*\/>/m.test(line);
 }
 
+// Throws if `__ctHelpers` was found as an Identifier
+// in the source code.
+function checkCTHelperVar(source: string) {
+  const sourceFile = ts.createSourceFile(
+    "source.tsx",
+    source,
+    ts.ScriptTarget.ES2023,
+  );
+  const visitor = (node: ts.Node): ts.Node => {
+    if (ts.isIdentifier(node)) {
+      if (node.text === CT_HELPERS_IDENTIFIER) {
+        throw new Error(
+          `Source cannot contain reserved '${CT_HELPERS_IDENTIFIER}' symbol.`,
+        );
+      }
+    }
+    return ts.visitEachChild(node, visitor, undefined);
+  };
+  ts.visitNode(sourceFile, visitor);
+}
+
 function getCTHelpersIdentifier(
   statement: ts.Statement,
 ): ts.Identifier | undefined {
diff --git a/packages/ts-transformers/test/transform.test.ts b/packages/ts-transformers/test/transform.test.ts
index 2cf4777b4..84ab9b432 100644
--- a/packages/ts-transformers/test/transform.test.ts
+++ b/packages/ts-transformers/test/transform.test.ts
@@ -1,5 +1,5 @@
 import { describe, it } from "@std/testing/bdd";
-import { assert } from "@std/assert";
+import { assert, assertRejects } from "@std/assert";
 import { transformFiles } from "./utils.ts";
 
 const fixture = `
@@ -34,3 +34,37 @@ describe("CommonToolsTransformerPipeline", () => {
     );
   });
 });
+
+describe("CTHelpers handling", () => {
+  it("Throws if __ctHelpers variable is used in source", async () => {
+    const statements = [
+      "function __ctHelpers() {}",
+      "function foo(): number { var __ctHelpers = 5; return __ctHelpers; }",
+      "var __ctHelpers: number = 5;",
+      "declare global { var __ctHelpers: any; }\nglobalThis.__ctHelpers = 5;",
+    ];
+
+    for (const statement of statements) {
+      await assertRejects(() =>
+        transformFiles({
+          "/main.ts": fixture + `\n${statement}`,
+        })
+      );
+    }
+  });
+
+  it("Allows '__ctHelpers' in comments and in other forms", async () => {
+    const statements = [
+      "var x = 5; // __ctHelpers",
+      "// __ctHelpers",
+      "/* __ctHelpers */",
+      "var __ctHelpers123: number = 5;",
+      "declare global {\nvar __ctHelpers1: any;\n}\nglobalThis.__ctHelpers1 = 5;",
+    ];
+    for (const statement of statements) {
+      await transformFiles({
+        "/main.ts": fixture + `\n${statement}`,
+      });
+    }
+  });
+});