The three clues that lead Holmes to conclude who Spalding's real identity is are:
- Appearance: short, stout, quick, and no facial hair
- There is a white splash of acid on his forehead
- Pierced ears for wearing earings from a Gypsy
There are five clues in total in the novel that Holmes uses to solve the mystery:
- Spalding was frequently in the cellar
- From 10am-2pm, Jabez was at his job with the red-headed league
- The ground in front of Jabez's pawn shop is solid
- Spalding's knees were covered with soil
- Jabez's pawn shop is located behind the City and Suburban Bank
Holmes also observed:
- The Red-Headed League appeared shortly after Jabez hired Spalding.
- Spalding encouraged Jabez to remain in line when he found everyone in the city with a trace of red in their hair had responded to the ad in the paper.
These clues told Holmes that Spalding may not be who he seemed to be. The clues listed by crmhaske identified confirmed Spalding's identity. The 5 clues related to what Spalding was doing, and the shop's location relative to the bank told Holmes what Spalding and the fictitious Red-Headed League were up to.