Charlie was six years old, stood at 3'4" and he weighed about 58 lbs. Charlie also suffered from a hereditary, genetic defect: hypophosphatemia. This caused Charlie's bones to become very brittle and is what caused him to be small in his height and weight. His hereditary defect is passed down from mothers; this led to the discovery that Margaret Sanders wasn't actually his biological mother and that she kidnapped him when he was an infant.
Charlie's biological mother, Jeannine Downey, was a drug addict who possessed hypophosphatemia which she passed down to her child. Charlie's real name was Nathan. His adoptive mother, Margaret Sanders, had gotten him in as a foster child at 10 days old as his mother was arrested on a drug charge. Three weeks later, the charges were dropped and Margaret gave him back. Margaret kept in touch with Jeannine to "make sure he was safe" and bought him things such as formula and a stroller. On Christmas Day, she found Jeannine on the kitchen floor dead, overdosed with a needle stuck in her arm. Margaret had heard Charlie crying upstairs and she promised him that she would never leave him alone again; he stopped crying. She kidnapped Charlie, though her intentions were good. During the interrogation of Charlie's murder, she also said she waited for Child Services to come and get him, but they never did.
Charlie was murdered by Edward Nelson in a sexual-assault-gone-bad. The two are interrupted by a group of teenagers, and Edward Nelson kneels on Charlie's chest in order to keep him quiet. Nelson's body weight compressed Charlie's chest, which caused his sternum to snap. His body was found about two days later behind a mall in the D.C. area. His case was very hard for the Jeffersonian team to work on due to Charlie's young age. Nelson was eventually arrested for Charlie's sexual assault and murder and confessed. Charlie's true parentage came to light during the investigation, resulting in Margaret being arrested for his kidnapping. She was eventually released and reunited with Shawn and David. After the murder was solved, Charlie's body was loaded into a small coffin by an emotional Zack Addy, who had been particularly affected by the case and taken away.