diff --git a/arch/ia64/pci/pci.c b/arch/ia64/pci/pci.c
index e643373e4701..729298f4b234 100644
--- a/arch/ia64/pci/pci.c
+++ b/arch/ia64/pci/pci.c
@@ -371,8 +371,6 @@ pci_acpi_scan_root(struct acpi_device *device, int domain, int bus)
 	 * such quirk. So we just ignore the case now.
 	 */
 	pbus = pci_scan_bus_parented(NULL, bus, &pci_root_ops, controller);
-	if (pbus)
-		pcibios_setup_root_windows(pbus, controller);
 
 	return pbus;
 
@@ -490,6 +488,8 @@ pcibios_fixup_bus (struct pci_bus *b)
 	if (b->self) {
 		pci_read_bridge_bases(b);
 		pcibios_fixup_bridge_resources(b->self);
+	} else {
+		pcibios_setup_root_windows(b, b->sysdata);
 	}
 	list_for_each_entry(dev, &b->devices, bus_list)
 		pcibios_fixup_device_resources(dev);