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Background: The prevalence of allergy‐related diseases (ARDs), including rhinitis, allergic conjunctivitis and eczema, is on the increase globally. The causes of this increase are not well established. Objectives: To investigate the risk factors associated with ARDs among schoolchildren in Uganda. Methods: We conducted a secondary data analysis of a large asthma case–control study involving 1700 schoolchildren, 5–17 years, in urban Uganda. ARDs were defined according to the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire. Skin prick testing (SPT) was conducted using standard procedures and allergen‐specific IgE (asIgE) using ImmunoCAP®. We employed inverse probability weighted analysis to generate estimated prevalence data and weighted odds ratios. Results: The lifetime estimated weighted prevalence of reported rhinitis, allergic conjunctivitis and eczema was 43.3%, 39.5% and 13.5%; weighted prevalence in 12 months was 10.1%, 9.1% and 2.3%, respectively. There was overlap of ARDs, with 66.3% of 1193 schoolchildren who reported having ever an ARDs (including asthma) reporting two or more. Risk factors associated with reported rhinitis in the last 12 months were city residence at birth [adjusted odds ratio (95% confidence interval) 2.66 (1.42–4.99) compared to rural]; father's [2.62 (1.79–3.83)] and mother's history of allergic disease [2.12 (1.48–3.02)]; frequent de‐worming in the last 12 months [2.01 (1.30–3.11), ≥2 versus none]; current high frequency of 'trucks passing on the street near home' [2.59 (1.48–4.52), 'almost all the time' versus rarely] and positive SPT [1.54 (1.09–2.18)] but not asIgE [1.38 (0.60–3.15)]. The same pattern of risk factors was observed for allergic conjunctivitis and eczema. Conclusion: We found extensive multi‐morbidity of, and overlap in the risk factors for, rhinitis, conjunctivitis and eczema—similar to asthma risk factors—among schoolchildren in urban Uganda. This suggests a similar underlying cause for all ARDs, associated with exposure to urban lifestyles and environment in Uganda. [ABSTRACT FROM AUTHOR]