- Mongrel Custom "Arm The Homeless" - Morello's most famous guitar, and his main guitar for standard tuning since 1986.
- Fender Stratocaster "Soul Power" - Originally made as a Factory Special Run for Guitar Center, Morello found it on the rack and really liked the look of it.
- Fender Telecaster, "Sendero Luminoso" - A black stock 1982 Standard Telecaster, his main guitar for use in drop-D in Rage Against the Machine, Audioslave and Street Sweeper Social Club. He got this guitar in a trade with his roommate.
- Fender Telecaster 2. Morello used this guitar when he played with Fistful of Mercy on Conan.
- Ibanez Artstar Hollowbody (Custom) - Made especially for Morello.
- Goya Rangemaster de Greco, "St. George Creamy" - Bought by Morello at a Canadian pawnshop for $60.
- Ibanez Talman (Custom)
- Gibson EDS-1275 (Double Neck SG) - Tuned to drop-D on the 6-string neck.
- Ovation Breadwinner - Tuned to standard E
- Gibson "Budweiser" Les Paul - Used during the recording of Audioslave's third album, Revelations.
- Gibson Les Paul Standard
- James Trussart Steelcaster
- "Whatever It Takes" guitar - A custom Ibanez Galvador classical acoustic guitar he uses during concerts as The Nightwatchman.
- "Black Spartacus" guitar- A black Gibson steel string acoustic guitar used as The Nightwatchman.
- Tanglewood Acoustic Guitar.
- Gibson Explorer II- This was Tom's main guitar in college.
- Kay guitar- Tom's first electric guitar, Morello bought this guitar for $50, his mother bought him an amp.