Although dyslipidemia is common after solid organ transplantation (Tx), there are few long-term studies in children. We investigated the prevalence of dyslipidemia up to 5 years after Tx in 125 children on triple immunosuppression with one of three different well-functioning grafts, kidney, liver, and heart, and 181 controls. Total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) concentrations were measured annually. Low-density lipoprotein cholesterol concentrations were also calculated. The risk factors for dyslipidemia were determined at 3 years. There was a high prevalence of hypertriglyceridaemia in all three groups, 50% in the kidney transplantation (KTx) and heart transplantation (HTx) groups and 30% in the liver transplantation (LTx) group. In addition, 50% of KTx patients had high TC. In the Tx groups taken together, the following independent associations were observed: KTx and high pre-Tx TC were associated with high TC, high trough concentration of blood cyclosporine with low HDL-C, and older age at Tx accounted for higher TG. Dyslipidemia, especially hypertriglyceridaemia, was common 3-5 years after Tx. The aetiology is multifactorial and depends on the transplanted organ.