The blood was found in the basement early in the investigation into Ayla Reynolds' disappearance from her father's home in Waterville, spokesman Steve McCausland said. The state crime laboratory has been running tests on it since then, but it was unclear when the test results would be ready.
Ayla's whereabouts have been unknown since her father, Justin DiPietro, reported her missing the morning of Dec. 17.
McCausland called the discovery of the blood "troubling."
"We have questioned the three adults that were there in the home that night," McCausland told The Associated Press. "We believe they have not given us the full story."
Ayla was 20 months old when she disappeared. DiPietro told police she was wearing green pajamas with polka dots and the words "Daddy's Princess" on them and had a soft cast on her broken left arm when he put to bed Dec. 16. He said she wasn't there the next morning.
Ayla had been staying with her father at the time. Her mother, Trista Reynolds, lives in Portland.
A vigil in her honor was being held Saturday in downtown Waterville.
The discovery of the blood, first reported Saturday by WCVB-TV in Boston, is the latest development in the investigation.
McCausland declined to discuss how much blood was found in the basement or how old it might have been. The blood was one of hundreds of pieces of potential evidence that were removed from the house where DiPietro lives with his mother, McCausland said.
Justin DiPietro did not immediately return a message left on his cellphone. Trista Reynolds was participating in Saturday's vigil and wasn't available for comment.
A woman who answered DiPietro's mother's cellphone hung up after being asked about the blood.
Ronald Reynolds, who is Trista Reynolds' father, said DiPietro hasn't been forthcoming with his version of what happened or what he knows. DiPietro has said he took a polygraph test, but has declined to say what the results were.
"They haven't given the full story, but this family has gone through so much pain, so much hurt," said Reynolds, who lives in Portland. "We're going into two months now and don't know anything, and all we get is the runaround."