Although it did not parallel the commercial success of the band's previous album, Things Fall Apart, the album reached number 28 on the US Billboard 200 chart and sold steadily, remaining on the chart for 38 weeks. On June 3, 2003, it was certified gold by the Recording Industry Association of America, for shipments of 500,000 copies in the United States. Upon its release, Phrenology received universal acclaim from music critics, who praised its musical direction and lyrical themes, and it was included in numerous publications' year-end lists of the year's best albums.
Following the breakthrough success of Things Fall Apart (1999), its release was highly anticipated and delayed, as recording took two years. The album is named after the discredited pseudoscience of phrenology, the study of head shapes to determine intelligence and character, which was used to rationalize racism during the 19th century in the United States. Its cover art was created by artist/printmaker Tom Huck.
On "Something in the Way of Things (In Town)", Amiri Baraka performs a poem about how the spirit of death and decay permeates African-American urban experiences. Set to a fusion of several African-American music influences, his poem observes "something in the way of our selves" and uses unusual imagery such as death "riding on top of the car peering through the windshield" and a "Negro squinting at us through the cage" with a smile "that ain't a smile but teeth flying against our necks".
Phrenology received widespread acclaim from critics. At Metacritic, which assigns a normalized rating out of 100 to reviews from mainstream publications, the album received an average score of 87, based on 23 reviews.Mojo magazine hailed it as a "masterpiece", while Rolling Stone writer Pat Blashill said it has "a startling array of hip-hop reinventions". Dave Heaton from PopMatters called Phrenology "an impressive, ambitious work" that shows the Roots "filling their sound out and pushing it in a variety of directions", with a form of "tight soul/funk" that "sounds even more exact, funkier and edgier" than on Things Fall Apart. 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".Blender's RJ Smith called it "a celebration of self-determination, a nonstop joyride through some very complicated brains". Jeremy Gladstone from Kludge felt the Roots had combined "complicated beats" with "complex lyrics" to produce a "shockingly honest sound". In The Guardian, Alexis Petridis found the group "exclusively capable of absorbing other genres", while the "more straightforward hip-hop" is "idiosyncratic and hugely enjoyable".Slant Magazine's Sal Cinquemani called the album "subtly progressive" and felt the lyrics "challenge the commodification and subsequent destruction of hip-hop culture".
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".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." He also called it the band's "hardest-hitting" album because they successfully "re-create their concert punch in the studio." In his column for The Village Voice, Robert Christgau believed the Roots have finally discovered how to write tuneful and structured music on Phrenology, as they "humanize their formal commitment with injections of singing and guitar".
At the end of 2002, Phrenology was named one of the year's best albums; according to Acclaimed Music, it was the 18th most ranked record on critics' year-end lists. It was voted the seventh best album of 2002 in The Village Voice's Pazz & Jop, an annual poll of American critics.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".