Three others sustained head injuries.
The two gored men were from the southeastern town of Valencia, aged 29 and 34, and were injured in an alleyway leading to the bullring. No further details were revealed.
The three others with head injuries, also Spaniards from Murcia, Madrid and Barcelona, were hospitalized. The latter, aged 36, was under observation and the two others were in fair condition.
More than 1,000 participants packed the narrow cobblestoned streets of Pamplona's old town. The bulls came out strong from the starting gate and completed the 850-meter run within 2 and a half minutes.
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One of the runners, on a fence, was charged head-on by a bull but was still able to clear the running lane by rolling under a railing after falling. Another runner avoided goring but was flipped violently and hit head his head hard against the ground.
Initial medical reports said that there were three head injuries but no gorings. Some participants at today's bull run wore black armbands in honor of 29-year-old matador Victor Barrio, who was fatally gored yesterday during a bullfight in eastern Spain.
Ten people, including four Americans, were gored in the San Fermin festival last year. In all, 15 people have died from gorings in the festival since record-keeping began in 1924.