Aim To examine relationships between subgingival biofilm composition and levels of gingival crevicular fluid (GCF) cytokines in periodontal health and generalized aggressive periodontitis (GAP). Materials and methods Periodontal parameters were measured in 25 periodontally healthy and 31 GAP subjects. Subgingival plaque and GCF samples were obtained from 14 sites from each subject. 40 subgingival taxa were quantified using checkerboard DNA-DNA hybridization and the concentrations of 8 GCF cytokines measured using Luminex. Cluster analysis was used to define sites with similar subgingival microbiotas in each clinical group. Significance of differences in clinical, microbiological and immunological parameters among clusters was determined using the Kruskal-Wallis test. Results GAP subjects had statistically significantly higher GCF levels of interleukin-1β (IL-1β) (p<0.001), granulocyte-macrophage colony-stimulating factor (GM-CSF) (p<0.01), and IL-1β/IL-10 ratio (p<0.001) and higher proportions of Red and Orange complex species than periodontally healthy subjects. There were no statistically significant differences in the mean proportion of cytokines among clusters in the periodontally healthy subjects, while the ratio IL-1β/IL-10 (p<0.05) differed significantly among clusters in the aggressive periodontitis group. Conclusions Different subgingival biofilm profiles are associated with distinct patterns of GCF cytokine expression. Aggressive periodontitis subjects were characterized by a higher IL-1β/IL-10 ratio than periodontally healthy subjects, suggesting an imbalance between pro- and anti-inflammatory cytokines in aggressive periodontitis.