In all studies of health-related problems and their effects on well-being, research design issues threaten to compromise the validity of findings. This is particularly so in a longitudinal study, essentially stemming from the tension between maintaining participant compliance and retaining investigator objectivity. Such a tension may be exacerbated where measures of dependent variables such as self-esteem are used alongside the collection of physical data which is essential to the study, as in research into the psychological effects of short stature on children and young people. In this paper one particular project, the Wessex Growth Study, is used to illustrate the common threats to validity, both internal and external, of such research, and to consider future improvements in design. The Wessex Growth Study, set up in 1986, was designed to overcome some of the methodological problems found in earlier research with short stature children. It is following the growth and psychological development through their school years of a cohort of short children (below third centile for height when first identified) and case-matched controls (10th-90th centiles) recruited at school entry (ages 5/6). Findings have generally found only small differences between short and average height children. Though these results so far have mainly been presented cross-sectionally, the young people involved are followed up at 6-monthly intervals for height and other data to be collected, and thus to some extent the study also has the advantages and problems of a longitudinal research design. Using Campbell and Stanley's criteria this article makes clear the strain on both internal and external validity in the study, but argues that these problems are to some extent inherent in all longitudinal psychological research, and are outweighed in the present research by the collection of data on short stature which would not otherwise be available. Future data collection within the study will introduce further improvements in design.