Aim: This study investigated whether allergies among schoolchildren increased in Sweden between 1979 and 2007 and whether the geographical differences observed in previous studies remained. Methods: We collected questionnaire data on asthma, allergic rhinoconjunctivitis (ARC) and eczema in children aged seven to eight years from Molndal, Gothenburg, in south-western Sweden and Kiruna in northern Sweden in 1979 (n = 4682), 1991 (n = 2481) and 2007 (n = 1029). The same regions and questions were used in all three studies, and extra questions on food allergy or intolerance were added in 2007. Results: In 1979, 1991 and 2007, the total prevalence of asthma was 2.5%, 5.7% and 7.1%, ARC was 5.5%, 8.1% and 11.1% and eczema was 7.1%, 18.3% and 19.7%, respectively. Asthma prevalence remained higher in Kiruna, but no significant regional differences were seen for ARC and eczema. Almost 20% reported a history of food allergy or intolerance, with a higher prevalence in Kiruna. The allergy risk was reduced if both parents were born outside Sweden. Conclusion: The prevalence of ARC continued to increase between 1991 and 2007, but increases in asthma and eczema started to level off in 1991. Some geographical differences remained, but total allergy rates were similar in Kiruna and Molndal in 2007.