When Sherlock Holmes is inspecting the bedrooms at Stoke Moran, he finds many clues. In Helen Stoner's room he finds a ventilator that only leads into Dr. Roylott's room next door rather than to the outside, as such a ventilator should. Holmes also discovers that the bell-rope beside Helen's bed is a dummy and that the bed is firmly secured to the floor with bolted clamps. These are three important clues. The ventilator was installed on purpose to enable Roylott to send his deadly snake into the sleeping girl's room. The bell-rope was installed to give the snake a way to slip directly down onto the girl's bed. And the bed was clamped to the floor so that it could not be moved away from its position by the bell-rope and directly below the ventilator.

In Dr. Roylott's room Holmes finds a locked steel safe with a saucer of milk on top of it. In addition, a third clue catches his eye:

The object which had caught his eye was a small dog lash hung on one corner of the bed. The lash, however, was curled upon itself and tied so as to make a loop of whipcord.

The snake is being kept in the steel safe. The milk is used to train the snake to come back through the ventilator when Roylott blows his whistle. The looped dog lash is used to recapture the dangerous snake when it emerges through the ventilator. At the climax of the story, when Holmes whips the snake with his cane, it retreats more quickly than Roylott expected. He is killed by the snake, and Holmes and Watson discover his dead body when they enter his room.