In 1999, Dan and Paul released their debut concept album So... How's Your Girl? via Tommy Boy label, loosely based on 'The Prettiest Week of My Life,' an episode from a short-lived Fox sitcom Get a Life (1990–92). The band was named after a fictional Handsome Boy Modeling School, where Chris Elliott's character enrolled to become a male model. The album is notable for a very eclectic line-up of guest rappers, vocalists, co-producers, comedians, and featured musicians from different eras and a variety of genres not necessarily associated with hip hop. Some of the participants include Del Tha Funkee Homosapien, J-Live, DJ Shadow, Mike D of the Beastie Boys, Don Novello as Father Guido Sarducci, Biz Markie, Dave Jolicoeur of De La Soul, Kid Koala, DJ Quest (2), Sean Lennon, Miho Hatori of Cibo Matto, Róisín Murphy, Money Mark, Encore, Sensational, Grand Puba and Sadat X of Brand Nubian, Alec Empire and EL-P, and many others. One of the singles from the album, The Projects (P Jays), had been featured on Music From The Motion Picture Ocean's Eleven soundtrack in 2001.
The duo's second album, White People, was released in 2004 by Elektra. Handsome Boy Modeling School continued working with some collaborators from the debut album (De La Soul, Don Novello, Kid Koala, EL-P), but also greatly expanded the list of featured artists: Mike Patton, Pharrell Williams, RZA, Cedric Bixler-Zavala of The Mars Volta, Casual, Dres, Rahzel, Lord Finesse, Barrington Levy, John Oates, DJ Q-Bert, Sean Martin (2) from Cage, Grand Wizard Theodore, Jazzy Jay, Julee Cruise, Cat Power, Alex Kapranos of Franz Ferdinand, Chester Bennington and Mike Shinoda of Linkin Park, Chino Moreno (Deftones), Jack Johnson, Jamie Cullum, and comic Tim Meadows.
According to Prince Paul's 2006 Pitchfork interview, the band ceased all activities due to financial disagreement and internal conflicts between the two members. After Huston announced his retirement from the Handsome Boy Modeling School, no one from Nakamura's camp or label executives, not even a band manager, contacted him or gave any public comments.