There is mounting evidence that innate and adaptive immunity are critical for periodontal disease‐mediated bone resorption. These studies examined the role of B and CD4 T cells in adaptive immunity of rats infected with Aggregatibacter actinomycetemcomitans (Aa). Sprague‐Dawley male rats were fed Aa‐containing mash or control‐mash for 2 weeks. B and CD4 T cells were obtained from draining lymph nodes at 2, 4 and 12 weeks, postinoculation. Quantitative polymerase chain reaction‐based messenger RNA expression was conducted for 89 cytokine family genes. Disease‐relevance of the differentially expressed genes was assessed using a biological interaction pathway analysis software. B and CD4 T cells of Aa‐infected rats increased and were activated, resulting in enhanced isotype‐switched serum immunoglobulin G by 2 weeks postinoculation. Bone resorption was evident 12 weeks after Aa‐feeding. In B cells, interleukin‐2 (IL‐2), macrophage‐inhibiting factor, IL‐19, IL‐21, tumor necrosis factor (TNF), CD40 ligand (CD40L), CD70, bone morphogenetic protein 2 (BMP2), BMP3, and BMP10 were upregulated early; while IL‐7, Fas ligand (FasL), small inducible cytokine subfamily E1, and growth differentiation factor 11 (GDF11; BMP11) were upregulated late (12 weeks). BMP10 was sustained throughout. In CD4 T cells, IL‐10, IL‐16, TNF, lymphotoxin‐beta (LTβ), APRIL, CD40L, FasL, RANKL and osteoprotegerin were upregulated early, whereas IL‐1β, IL‐1RN, IL‐1F8, IL‐24, interferon‐α1, GDF11 (BMP11), and GDF15 were upregulated late (12 weeks). Adaptive immunity appears crucial for bone resorption. Several of the deregulated genes are, for the first time, shown to be associated with bone resorption, and the results indicate that activated B cells produce BMP10. The study provides a rationale for a link between periodontal disease and other systemic diseases.