Holmes comes across his first solid clue when he investigates the family background of the murdered woman and her sister Helen. Helen has already told him that their mother, unlike their stepfather, was wealthy and died in an untimely accident some years back. Holmes sets out to discover more. He comes across a copy of the mother's will, whereby he learns that she left a considerable allowance to both her daughters in the event of their marriage. Julia had been engaged when she died, and Helen has recently become engaged as well. Holmes therefore realises that as the marriage of his stepdughters would have left him 'with a mere pittance', Dr Roylott has taken steps to ensure the marriages do not take place. In other words, he contrived the murder of Julia and is planning the same for Helen. The mother's will thus provides Holmes with a vital clue to the identity of the murderer; it supplies a motive.
Secondly, when Holmes and Watson go to see the bedroom where Julia died, they discover very odd things about it. The bed is clamped to the floor, and beside it there is a bell-rope which does not ring any bell.There is also a small ventilator in the wall above the rope, even although there is another room next door. As Holmes wonders, why have a ventilator that just opens out into another room? It is also a matter of no small significance that the room next door is Dr Roylott's. Holmes concludes from all this that the clamped bed was used to trap Julia while the means of her death came down upon her as she slept - from the ventilator and down the false bell-rope.
A third clue lies in the nature of Dr Rolyott's lifestyle. Helen reveals that he once practised in India and has all manner of exotic pets sent over from there. Although Holmes somewhat uncharacteristically goes off on the wrong track to begin with, thinking that the local gypsies have had a hand in Julia's death, he soon comes to realise that the culprit is actually a deadly Indian snake kept by Roylott and trained to go through the ventilator and down the bell-rope. Apparently its poison is not readily traceable, so that the real cause of Julia's death was missed. (It must be remembered that post-mortem examinations at the time when this story was written were not as advanced as they are now.) Holmes and Watson get to see the snake in action for themselves when it kills Roylott, finally putting an end to his nefarious activities.