Genetic polymorphisms of cytokines have been associated with the susceptibility, severity, and clinical outcome of inflammatory diseases, such as periodontitis and chronic arthritis. An important question to address is how interleukin (IL)-1 polymorphisms affect the cytokine profiles of patients with such diseases. The study population consisted of Danish white adults, <35 years of age, who were diagnosed with localized aggressive periodontitis (LAgP, n = 18), generalized aggressive periodontitis (GAgP, n = 27), juvenile idiopathic arthritis (JIA, n = 10), and rheumatoid arthritis (RA, n = 23) and healthy individuals with no systemic or oral diseases (n = 25). Genotypes of IL-1A-889, IL-1A+4845, IL-1B-511, and IL-1B+3954 were determined by polymerase chain reaction (PCR)-restriction fragment length polymorphism, and IL-1RN variable number tandem repeat (VNTR) was detected by PCR amplification and fragment size analysis. Analysis of variance was used to evaluate the effects of IL-1 genotypes on the levels of IL-1alpha, -1beta, -1 receptor antagonist, -6, and -10; tumor necrosis factor-alpha (TNF-alpha); and lymphotoxin-alpha in peripheral blood (plasma) and in unstimulated and stimulated whole blood cell cultures from the same blood collection. The frequencies of IL-1 genotypes investigated did not differ significantly between diseased and control individuals. In LAgP patients, allele 2 of IL-1RN VNTR was associated with significantly higher levels of IL-1alpha, -6, and -10 and TNF-alpha, whereas allele 2 of IL-1B+3954 was associated with significantly lower levels of the same cytokines. In GAgP patients, a general lack of association was found. In JIA and RA patients, IL-1RN VNTR also influenced the cytokine levels. IL-1 genotypes were associated with cytokine levels in patients with aggressive periodontitis and chronic arthritis. No associations were observed in control individuals.