Soon after the murders, Lizzie emerged as the prime suspect after John Morse's alibi checked out. She then was arrested and tried on three counts, the murder of Abbey, of Andrew, and of them both and, if found guilty, faced death by hanging. Six days after the murders occurred, she went to court. The all-male jury was put into a difficult position. It was the Victorian Era where women were considered delicate flowers and not capable of killing someone and it was not a common or working class woman they were to judge guilty or innocent, it was a wealthy society lady. After only an hour of deliberating, the jury declared Lizzie to be not guilty. It is said it only took them 15 minutes to decide, but out of respect for the prosecution, they waited another 45 minutes before they informed the court of their decision. What makes the Fall River murders so perplexing is that the motive, the weapon and the opportunity for such a crime are all seemingly absent. When the Fall River constabulary investigated the murders, they found no money or jewelry missing, not even small amounts of change or the packet of bus tickets as were taken in the daytime break-in at the Borden home twelve months earlier. Later, Prosecuting Attorney Knowlton hired a machinist who spent two days cracking open Andrew Borden's safe in hopes of finding a missing will disinheriting both daughters. But Borden died intestate, leaving Lizzie and Emma to inherit his entire fortune. Besides the lack of a clear motive for the murders, there was also the disconcerting lack of opportunity. Fall River found the entire Borden house locked up as usual, and during the two-and-a-half-hour period in which both murders were completed, the maid Bridget was outside the house washing windows and daughter Lizzie was inside the house reading a magazine. Even if one of the two committed the crime, the violent and bloody act should have been noisy enough to attract the attention of the other.
