Lipinski's professional skating career was hampered by a series of hip injuries. In August 1998, Lipinski suffered a hip injury in practice for Stars on Ice. In September 2000, she underwent surgery to repair a torn labrum in her hip. She said her hip problem had been misdiagnosed for several years. Lipinski suffered another hip injury in 2002 during a Stars on Ice show in St. Louis, when she fell hard on her right hip during a jump, and then tore muscles around the bruised area the next day.
Many people have pointed to the repetitive stress of practicing the triple loop combinations Lipinski performed during her competitive days as the primary cause of her hip problems. Lipinski herself has issued contradictory statements about the timing, cause, and severity of her injuries. After her surgery in 2000, she stated in interviews that the real reason she had turned professional was that she had originally incurred the injury to her hip in the summer of 1997 and that she had skated the entire Olympic season in terrible pain, contradicting her earlier account of the original injury having occurred in the summer of 1998 rather than in 1997. In a 2010 statement on her web site, Lipinski denied that her hip injury was a factor in her decision to retire or that she suffered particular pain during her amateur career beyond "the norm for any athlete."