Photodynamic therapy (PDT) is a promising and emerging noninvasive treatment modality for the treatment of a great number of malignant and non-malignant diseases. Therapeutic strategy in PDT is performed by combining a photosensitizer which can potently and specifically kill diseased cell and a light source, preferentially near-IR light (650-800 nm). In spite of the fact that numerous studies have been published and notable progress has been made in tumor biology and photochemistry which let us to design novel therapeutic agents, the number of the new therapeutic agents which have been recently got approval for clinical application are relatively low. We aimed to produce novel photosensitizers. In the chapters 3, 4 and 5 BODIPY dyes which are amenable to functionalization have been used to produce a novel series of BODIPY-based photosensitizers. We synthesized and characterized a series of novel BODIPY-based photosensitizers. The first part describes novel near-IR BODIPY-based photosensitizers. In the second part, the main goal was to design and synthesize heavy atom free BODIPY-based photosensitizers. In this respect, a new modification of the BODIPY dyes, novel orthogonal BODIPYs were synthesized and their computational analysis were done. A cell culture assay with cancer cell lines was performed in order to demonstrate photocytotoxicity of the orthogonal BODIPY. The third study underlines the importance of micelle-embedded BODIPY-based photosensitizers for photodynamic therapy.