In May 2004, Mueller was diagnosed with throat cancer, and a benefit concert was held to help him with his medical bills. In September of that year, Grant Hart and Bob Mould of Hüsker Dü reunited for the first time in seventeen years at the Rock for Karl benefit in Minneapolis. Paul Westerberg also made an appearance, as did Soul Asylum, in Mueller's last public performance. Mueller died of cancer in June 2005. Mueller was subsequently cremated and his remains reside at Lakewood Cemetery in Minneapolis. His widow, Mary Beth, resides in Minneapolis.