In affirming Vallejos conviction, the high tribunal ruled that the result of DNA testing a scientific technique of identifying the genetic code of an individual is now admissible as evidence in all courts of law nationwide.
"Taken together with the other circumstantial evidence, especially the DNA profile found in the vaginal swabs taken from the victim which matched the DNA profile of Vallejo, prove beyond reasonable doubt Vallejos guilt," read part of the tribunals decision.
Using DNA or deoxyribonucleic acid, the US Supreme Court has set free 80 death convicts after evidence showed that they were not guilty of the crime they were accused of committing.
The uniqueness of an individuals DNA which contains his genetic code or profile much like a fingerprint, can identify one person from another.
The Supreme Court threw out the arguments of Vallejos lawyer that DNA was a "mere junk science" because the basis of his clients conviction was an "unreliable" tool.
"This generalization about the state of DNA science in the Philippines, like Vallejos fulmination against hardened policemen who leave no marks of torture on their victims, is without any basis," read the decision.
Last May 9, the Supreme Court en banc affirmed the 2000 decision of Judge Christopher Lock (now deputy court administrator) of the Cavite Regional Trial Court, for Vallejo to pay his victims heirs in the amount of P100,000 as civil indemnity and P50,000 as moral damages.
"Among the evidence which established the guilt of Vallejo was the DNA analysis done by the National Bureau of Investigation on the vaginal swabs collected from the victim and found to have DNA profiles of Vallejo," read a statement from the Supreme Court public information office.
During trial, Vallejo said police forced him to produce the blood-stained clothes which he was said to have used in raping his victim.
Vallejos blood type ("O") matched those on the clothes after the NBI took blood samples from him when they were investigating his involvement in the crime.
But the Supreme Court said Vallejo failed to prove that policemen tortured him and that a search warrant was no longer needed then because he had allowed police to search his house.
Court records showed that at around 1 p.m. on July 10, 1999, the victim went to the house of Vallejos sister who was her tutor.
After an hour, the victim went out with Vallejo, who was staying at the same house, to look for a book which she could use for a school project.
They later returned to the house of Vallejos sister after they had found the book.
When the victims mother woke up at 5 a.m. without finding her daughter, she went to the house of Vallejos sister but was told that the victim had already left.
The victims mother searched for her until early morning the following day.
At 10 a.m., she was informed that her daughters dead body had been found tied to the root of an Aroma tree by the river bank, with her sleeveless shirt tied around her neck.
After barangay officials picked up Vallejo and took him to the barangay hall, the victims mother pointed to him as a suspect because he was the last person seen with her daughter.