BACKGROUND: The prevalence of childhood asthma in Scotland is one of the highest in the world. The morbidity secondary to allergic diseases is significant in terms of costs to the nation and effects on the family including the child. AIMS: The aims of this study were to describe the prevalence of asthma, eczema and hay fever in the Highlands of Scotland and in the Shetland Isles and to examine factors in relation to quality of life and social deprivation. METHOD: A total population survey of 12 year old children using a parent completed questionnaire. RESULTS: 86.3% (2658/3080) returned questionnaires. Of the 2549 questionnaires analysed, 476 (18.7%) reported asthma ever, 362 (14.2%) wheeze in last 12 months, 508 (19.9%) reported hay fever ever and 555 (21.8%) reported eczema ever. Of the children reporting asthma or wheeze, 35.4% (229/647) had missed school because of asthma or wheeze, 38.0% (246/647) had missed physical education. 62.5% (354/566) of subjects with wheeze ever reported sleep disturbance. Deprivation measured by DEPCAT scores was associated with maternal smoking and bronchitis in the child but not with allergic diseases. CONCLUSION: Compared with previous studies, the prevalence of asthma was unchanged but eczema has increased in Highland adolescents. Allergic disease has a significant impact on school attendance and physical activity. Deprivation was associated with maternal smoking and bronchitis in the child but not with allergic diseases. The impact of allergic diseases in rural areas may be different from urban areas.