Most uninfected children born to diagnosed HIV-infected women in the United Kingdom (UK) are exposed to antiretroviral therapy (ART) in utero and neonatally, and concerns exist about potential adverse effects of such exposure. We explored the feasibility of using national clinic-based follow-up to investigate the association between ART exposure and adverse health events occurring after the neonatal period. Active surveillance of obstetric and paediatric HIV infection is conducted through the National Study of HIV in Pregnancy and Childhood (NSHPC). Between 2002 and 2005, health professionals enrolled previously notified uninfected children in a consented follow-up study (the CHildren exposed to AntiRetroviral Therapy (CHART) study). Follow-up information was collected opportunistically using a standard questionnaire. Of 2104 eligible uninfected children born in the UK between 1996 and 2004, 704 (33.5%) were enrolled in CHART; parents of 4.8% (100/2104) declined, 2.8% (59/2104) had gone abroad, 21.6% (455/2104) were not contactable, and the remaining 37.3% (786/2104) were not enrolled mainly because of lack of clinic resources or unwillingness of health professionals to approach the families. Demographic characteristics and type of ART exposure for enrolled and non-enrolled children were similar. Latest information on enrolled children was available at a median age of 24 months. Minor childhood ailments were reported in the majority of children, febrile seizures in 1.6% (11/704), and major health problems in 3.8% (27/704). It was reassuring that prevalence of these outcomes was within UK norms, but numbers were small and duration of follow-up was limited. The difficulties encountered in enrolling and retaining children in this study indicate that comprehensive clinic-based follow-up of ART-exposed uninfected children is not practical. Alternative approaches are required; a robust, secure data linkage protocol would provide a more feasible and sustainable system for long-term monitoring of in utero ART exposure.