In the last few years of his life, Cowsill was in declining health, suffering from emphysema, Cushing syndrome and osteoporosis. Cowsill's health went into serious decline in 2004. He required a cane to assist in walking, and underwent total hip replacement surgery and three major back surgeries, a complication from which resulted in a permanently collapsed lung. That year, a benefit concert for Cowsill was held in Los Angeles, featuring the Cowsills, Peter Tork, Susanna Hoffs and Shirley Jones, among others.