diff --git a/nix/guix-register/guix-register.cc b/nix/guix-register/guix-register.cc
index 0a028f0cfe..8f9c3c86ab 100644
--- a/nix/guix-register/guix-register.cc
+++ b/nix/guix-register/guix-register.cc
@@ -62,6 +62,10 @@ static const struct argp_option options[] =
     { 0, 0, 0, 0, 0 }
   };
 
+
+/* Prefix of the store being populated.  */
+static std::string prefix;
+
 /* Parse a single option. */
 static error_t
 parse_opt (int key, char *arg, struct argp_state *state)
@@ -70,8 +74,8 @@ parse_opt (int key, char *arg, struct argp_state *state)
     {
     case 'p':
       {
-	string prefix = canonPath (arg);
-	settings.nixStore = prefix + NIX_STORE_DIR;
+	prefix = canonPath (arg);
+	settings.nixStore = NIX_STORE_DIR;
 	settings.nixDataDir = prefix + NIX_DATA_DIR;
 	settings.nixLogDir = prefix + NIX_LOG_DIR;
 	settings.nixStateDir = prefix + NIX_STATE_DIR;
@@ -128,15 +132,25 @@ register_validity (LocalStore *store, std::istream &input,
       ValidPathInfo info = decodeValidPathInfo (input, hashGiven);
       if (info.path == "")
 	break;
+
+      /* Rewrite the input to refer final name, as if we were in a chroot
+	 under PREFIX.  */
+      std::string final_prefix (NIX_STORE_DIR "/");
+      info.path = final_prefix + baseNameOf (info.path);
+
+      /* Keep its real path to canonicalize it and compute its hash.  */
+      std::string real_path;
+      real_path = prefix + "/" + settings.nixStore + "/" + baseNameOf (info.path);
+
       if (!store->isValidPath (info.path) || reregister)
 	{
 	  /* !!! races */
 	  if (canonicalise)
-	    canonicalisePathMetaData (info.path, -1);
+	    canonicalisePathMetaData (real_path, -1);
 
 	  if (!hashGiven)
 	    {
-	      HashResult hash = hashPath (htSHA256, info.path);
+	      HashResult hash = hashPath (htSHA256, real_path);
 	      info.hash = hash.first;
 	      info.narSize = hash.second;
 	    }
diff --git a/tests/guix-register.sh b/tests/guix-register.sh
index b76a1af54f..ca28fb0d95 100644
--- a/tests/guix-register.sh
+++ b/tests/guix-register.sh
@@ -38,9 +38,10 @@ cp -r "$to_copy" "$new_store_dir"
 copied="$new_store_dir/`basename $to_copy`"
 
 # Create a file representing a closure with zero references, and with an empty
-# "deriver" field.
+# "deriver" field.  Note that we give the file name as it appears in the
+# original store, and 'guix-register' translates it to match the prefix.
 cat >> "$closure" <<EOF
-$copied
+$to_copy
 
 0
 EOF
@@ -49,26 +50,37 @@ EOF
 guix-register -p "$new_store" < "$closure"
 
 # Doing it a second time shouldn't hurt.
-guix-register -p "$new_store" "$closure"
+guix-register --prefix "$new_store" "$closure"
 
 # Now make sure this is recognized as valid.
 
 NIX_IGNORE_SYMLINK_STORE=1
 NIX_STORE_DIR="$new_store_dir"
-NIX_LOCALSTATE_DIR="$new_store$localstatedir"
+NIX_STATE_DIR="$new_store$localstatedir"
 NIX_LOG_DIR="$new_store$localstatedir/log/nix"
 NIX_DB_DIR="$new_store$localstatedir/nix/db"
 
-export NIX_IGNORE_SYMLINK_STORE NIX_STORE_DIR NIX_LOCALSTATE_DIR	\
+export NIX_IGNORE_SYMLINK_STORE NIX_STORE_DIR NIX_STATE_DIR	\
   NIX_LOG_DIR NIX_DB_DIR
 
 guix-daemon --disable-chroot &
 subdaemon_pid=$!
 exit_hook="kill $subdaemon_pid"
 
+final_name="$storedir/`basename $to_copy`"
+
 # At this point the copy in $new_store must be valid, and unreferenced.
+# The database under $new_store uses the $final_name, but we can't use
+# that name in a 'valid-path?' query because 'assertStorePath' would kill
+# us because of the wrong prefix.  So we just list dead paths instead.
 guile -c "
    (use-modules (guix store))
    (define s (open-connection))
-   (exit (and (valid-path? s \"$copied\")
-              (equal? (list \"$copied\") (dead-paths s))))"
+   (exit (equal? (list \"$copied\") (dead-paths s)))"
+
+# When 'sqlite3' is available, check the name in the database.
+if type -P sqlite3
+then
+    echo "select * from ValidPaths where path=\"$final_name\";" | \
+	sqlite3 $NIX_DB_DIR/db.sqlite
+fi