diff --git a/src/api/checkCompatibility.ts b/src/api/checkCompatibility.ts
index 874d5a2308..16fef07b34 100644
--- a/src/api/checkCompatibility.ts
+++ b/src/api/checkCompatibility.ts
@@ -67,6 +67,10 @@ export default function checkCompatibility (
     modulesPath: string,
   }
 ) {
+  // Important: comparing paths with path.relative()
+  // is the only way to compare paths correctly on Windows
+  // as of Node.js 4-9
+  // See related issue: https://github.com/pnpm/pnpm/issues/996
   if (path.relative(modules.store, opts.storePath) !== '') {
     throw new UnexpectedStoreError({
       expectedStorePath: modules.store,