[2] It was primarily produced by members of the band and features contributions from hip hop and neo soul artists such as Cody ChesnuTT, Musiq Soulchild, Talib Kweli, and Jill Scott.

[5][8][9][10][11] According to music critic Greg Kot, the Roots forge a connection between hip hop and neo soul on the album,[12] while Treble writer says it can "best be described" as progressive rap,[13] and Entertainment Weekly's Raymond Fiore calls it the band's "left-field rock-rap opus".

[26] In the Chicago Sun-Times, critic Jim DeRogatis gave the record four out of four stars and called it "a near-classic right out of the gate, an urgent, raucous and thought-provoking 70 minutes that mine the musical territory between hard hip-hop and smoother Philly soul".

[10] In a less enthusiastic review, Uncut magazine said Phrenology shows the Roots' "willingness to push the envelope of their organic jazz-rap" that is unparalleled but sometimes musically pretentious or indulgent, particularly on "Something in the Way of Things" and the coda to "Water".

[29] AllMusic editor Steve Huey felt it is "a challenging, hugely ambitious opus that's by turns brilliant and bewildering, as it strains to push the very sound of hip-hop into the future."

"[1] In his column for The Village Voice, Robert Christgau believed the Roots have finally discovered how to write tuneful and structured music on Phrenology,[24] as they "humanize their formal commitment with injections of singing and guitar".

[31] The Rolling Stone Album Guide (2004) later gave it four-and-a-half stars and cited "Water" as a highlight, "that begins with the age-old Bo Diddley beat and ends as an extended musique concrète-style instrumental fantasia".