The spirochete Borrelia burgdorferi s.l. can enter into different eukaryotic cells. Intracellular localization of bacteria may cause many changes in different cell pathways like apoptosis-mediated caspase cascade. The present studies focused on gene expression associated with caspase cascade after normal human dermal fibroblasts (NHDF) infection with Borrelia garinii, Borrelia afzelii, and B. burgdorferi s.s. The use of oligonucleotide microarray technique enabled an expression level comparison of genes associated with caspase cascade in NHDF infected with spirochetes. The increased expression of genes associated with caspase cascade was observed in case of CASP5, CASP2, CARD10, CASP10, MALT1, and NLRP1. The decreased expression was observed in case of CASP4, CASP6, and CASP1. The mRNA expression for CASP3 was inhibited in cells infected with three genospecies of Borrelia. However, the intensity of fluorescence was not statistically significant. In addition, cell cultures were fixed and procedure of caspase-3 detection and the TUNEL assay were performed. The in situ caspase-3 detection procedure confirmed the results obtained from microarray analyses. Only several fluorescent signals were observed. Many apoptotic cells were detected in NHDF-infected cultures with all spirochete genospecies found using the TUNEL reaction.