Deregulation of apoptosis can contribute to diverse pathologic processes. Understanding its regulatory mechanisms in endothelial cells (ECs) has great importance for the development of novel therapy strategies for cancer and cardiovascular pathologies. An oxidative stress with the generation of radical oxygen species (ROS) is a common mechanism causing ECs' dysfunction and apoptosis. The generation of ROS can be triggered by various stimuli including photodynamic therapy (PDT). The molecular mechanisms underlying PDT, and specifically Hypericin PDT (HypPDT), are not completely understood, although it has been shown that the sub-cellular Hyp localization and distribution determine which signaling pathway will lead to cell death. Cell responses to HypPDT are highly dependent on the Hyp intracellular localization and accumulation. The mechanisms by which ROS cause or regulate ECs apoptosis typically include receptor activation, caspase activation, Bcl-2 family proteins, and mitochondrial dysfunction. We were particularly interested in Bcl-2 family proteins and investigated their role in apoptosis of ECs triggered by HypPDT. In the present work, we show that the presence of Hyp itself has an effect on the distribution of Bcl2 family members. Presence of Hyp triggers translocation of Bax into mitochondria, and translocation of Bax and Bcl2 into nuclei in ECs. Further, HypPDT results in oxidative stress via mitochondrial superoxide production and primarily in necrotic type of death in HAEC cells. HAEC cell respiratory control is similar in control cells and in cells after 24 hrs incubation with Hyp without irradiation, suggesting that even though Hyp presence resulted in an increased number of apoptotic cells, the mitochondria function was not affected. However, HypPDT resulted in diminished OCR, indicating that HypPDT oxidative stress abolished mitochondria function in intact cells.