Adding another descendant if anyone cares:
$domdoc=new DOMDocument();
$domdoc->formatOutput=TRUE;
//print $domdoc->saveXML();
$empty_cart_xml=
'<Order xmlns="http://payments.amazon.com/checkout/2009-05-15/">
<Cart>
<Items>
<Item>1</Item>
<Item>2</Item>
<Item>3</Item>
</Items>
</Cart>
<OrderCalculationCallbacks>
<CalculateTaxRates>true</CalculateTaxRates>
<CalculatePromotions>true</CalculatePromotions>
<CalculateShippingRates>true</CalculateShippingRates>
<OrderCallbackEndpoint>
https://my.endpoint.com/receive.php
</OrderCallbackEndpoint>
<ProcessOrderOnCallbackFailure>true</ProcessOrderOnCallbackFailure>
</OrderCalculationCallbacks>
</Order>';
//print $empty_cart_xml;
$domdoc->loadXML($empty_cart_xml);
print $domdoc->saveXML()."<hr/>";
/*$xpath=new DOMXPath($domdoc);
$items=$xpath->query('/Order/Cart/Items[1]');
foreach($items AS $item)
{
$item->appendChild($domdoc->createElement('Item','4'));
}*/
$item=$domdoc->createElement('Item');
$domdoc->getElementsByTagName('Items')->item(0)->appendChild($item);
$price=$domdoc->createElement('Price','3.14');
$item->appendChild($price); //price is a descendant of this item
$domdoc->formatOutput=TRUE;
print $domdoc->saveXML();