The functional interaction between the immune system and bone metabolism has been established at both molecular and cellular levels. We have used non-parametric and multidimensional expression pattern analyses to determine significantly changed mRNA profile of immune system-associated genes in postmenopausal osteoporotic (OP) vs. non-osteoporotic (NOP) bone tissue. Seven bone tissue samples from OP patients and ten bone tissue samples from NOP women were examined in our study. The transcription differences of selected 44 genes were analyzed in Taqman probe-based quantitative real-time RT-PCR system. Mann-Whitney test indicated significantly down-regulated transcription activity of 3 genes (FCGR2A, NFKB1 and SCARA3) in OP bone tissue which have prominent role in (antibody) clearance, phagocytosis, pathogen recognition and inflammatory response. According to the canonical variates analysis results, the groups of postmenopausal OP and NOP women are separable by genes coding for cytokines, co-stimulators and cell surface receptors affected in innate immunity which have high discriminatory power. Based on the complex gene expression patterns in human bone cells, we could distinguish OP and NOP states from an immunological aspect. Our data may provide further insights into the changes of the intersystem crosstalk between the immune and skeletal systems, as well as into the local immune response in the altered microenvironment of OP bone.