The prevalence and characteristics of headache were studied in a national cohort of 177 pediatric patients with kidney, liver, and heart transplants. All patients received triple drug immunosuppression with CsA, Aza, and MP. Data on headaches were collected by sending two questionnaires and reviewing the medical records. Statements on headache were found in the medical records of 46% of the patients. According to a questionnaire, two thirds had experienced headaches sometime after transplantation, and 40% had present headaches. The episodes had significantly affected the quality of life in a third of the patients, and resulted in neurological examination in 15%. Most of the subjects (61%) described typical episode as mild or moderate, and 39% as severe or very severe. The usual episodes lasted <4 h in 73% of the patients and >4 h in 27%. The headache could be classified as migraine, probable migraine or headache without specific features in 33%, 31%, and 36%, respectively. Most patients (82%) had used pain-killers, mainly acetaminophen and ibuprofen. Headache episodes may significantly impair the quality of life in children and adolescents after organ transplantation.