Observation of percentages changes of lymphocytes (CD19), T(CD3), subsets CD4, CD8, NK cells, activated lymphocytes with fenotype CD3+HLA-DR, CD4/CD8 rate in Lyme borreliosis was carried out before (I examination) and after antibioticotherapy (II examination). 30 patients in aged 17-60 (x = 41) with recognition of erythema migrans(EM), Lyme arthritis(LA) and neuroborreliosis(NB) were examined. Epidemiological, clinical diagnosis was confirm by the presence of antibodies in ELISA test. Lymphocytes and their subsets, NK cells were signed and measured by flow cytometric immunophenotyping in Coulter EPIX XL with Becton-Dickinson antibodies twice: before and after treatment. Ampicillin, ceftriaxon or cefotaxim was applied during 4 weeks. AnStat program was used in statistic analysis. Value CD3 (x = 72.54) in I test was higher than control (x = 69.3), but CD19 (x = 13.2) was lower than control (x = 12.9). In II examination we stated CD19 (x = 9.48) progressive significant decreased in comparison to I examination. Percentage CD4 in II examination (x = 42) was lower than control (x = 45.8). Subset of CD8 had lower value in I examination (x = 28.03), as in II (x = 30.72) in comparison with control (x = 34.2). We showed lower CD4/CD8 (x = 1.40) rate after treatment than control (x = 2.67). We showed lower percentage NK cells after treatment (x = 13.5) than control. We also found lower percentage activated subsets T cells with phenotype CD3+HLA-DR before (x = 4.78) and after treatment (x = 4.03) compared with control (x = 7.27). No statistical changes in subsets with receptor for IL-2 before and after treatment was shown. In the course of active infection B.burgdorferi essential changes in lymphocytes subsets are observed. Decreased percentages of CD4, CD8, NK and CD3+HLA-DR+ in whole blood indicate their important role in immunopathogenesis of Lyme borreliosis. Lack of normalization of investigated parameters after treatment can be caused by inertion of elements immunologic system, as well as too short antibioticotherapies.