Background: The role of immunization with bacillus Calmette-Guérin (BCG) in the prevalence of asthma, hay fever and atopic dermatitis is not definitely established and seems to be influenced by ethnic background. The aim of this study was to analyze the relationship between this immunization and the prevalence of those diseases in a homogeneous population of Spanish schoolchildren. Methods: The International Study of Asthma and Allergies in Childhood (ISAAC) core and environmental questionnaires were used in four different centers of the Spanish North Atlantic coast. Bilbao, San Sebastián and Asturias have a universal BCG immunization policy during the first days of life, whereas La Coruña discontinued this practice in 1989. Except for this center, immunization coverage was above 90%. A random sample of schools of Asturias or all schools in the city district (rest of centers) with children 6 and 7 years old was surveyed. Results: The participation rate was above 70%. After excluding those children born outside Spain, the numbers were 6,762 immunized and 2,828 nonimmunized. After adjusting for gender, age, smoking habits of the father and mother, truck traffic near the household, older and younger siblings and having a cat or a dog during the first year of the child’s life, the adjusted ORs of the BCG-immunized children suffering from asthma, hay fever and atopic dermatitis were respectively 0.87 (95% CI 0.76–1.00), 0.87 (0.75–1.01) and 0.89 (0.76–1.05). Conclusions: BCG immunization offers a weak but significant protection against asthma and hay fever in Spanish schoolchildren.