The team has reached sockets that once held bluestones - smaller stones, most now missing or uprooted, which formed the site's original structure.
The researchers believe that the bluestones could reveal that Stonehenge was once a place of healing.
The dig is the first to take place at Stonehenge for more than 40 years.
The team now needs to extract organic material from these holes to date when the stones first arrived.
They believe that the bluestones, which were transported 250km from the Preseli Hills in Wales to the Salisbury Plain in Wiltshire, were brought to the site because the ancient people believed they had healing properties.