BACKGROUND: Allergic sensitization to Alternaria has been related to asthma in various studies, but its association with allergic rhinitis is still controversial. OBJECTIVES: The aim of this study was to assess at the population level the relationships in childhood between Alternaria sensitization and 'past-year rhinoconjunctivitis' (PYRC), 'ever hay fever' (EHF) and 'ever allergic rhinitis caused by allergens other than pollens' (EAR) according to the presence or the absence of asthma. METHODS: This study is part of the Six Cities Study, the French contribution to the International Study of Asthma and Allergies in Childhood (ISAAC) Phase II. Children underwent skin prick test (SPT) to Alternaria and parents filled a standardized medical questionnaire. RESULTS: Some 6726 children with a mean age of 10 years were examined. The overall prevalence of Alternaria sensitization was 2.8%, 0.8% for monosensitization. Prevalences of symptoms in sensitized children were 27.7% for PYRC, 27.0% for EHF and 30.4% for EAR. Adjusted Odds Ratios (OR) between Alternaria sensitization and allergic rhinitis phenotypes were 2.34 (95% confidence interval: 1.51-3.63) for PYRC, 2.40 (1.65-3.50) for EHF and 2.95 (2.05-4.23) for EAR. The relationship still remained in the case of monosensitization to Alternaria for both PYRC and EAR when excluding the asthmatic children [OR = 3.87 (1.54-9.78) and 2.88 (1.10-7.55) respectively]. CONCLUSION: In our population-based sample of children, we found a link between Alternaria sensitization and allergic rhinitis, independently of asthma, which is compatible with the mechanisms of deposition of Alternaria in the upper airways.