Photodynamic therapy provides the formation of reactive oxygen species that are capable of inducing cell death. Human laryngeal carcinoma (HEp-2) cells have been evaluated in this study under PDT treatment. Cells were treated with photosensitizer aluminum phthalocyanine tetrasulfonate (AlPcS4) and irradiated with a Biopdi/Irrad-Led5 660 LED with 660 nm wavelength, intensity of delivered light of 25 mW/cm2, power of 70 mW, fluence of 5 J/cm2 for 24 h and 48 h, and then evaluated. Cell population was not increased by PDT treatment after the tested period. The apoptosis assay demonstrated that control groups exhibit approximately 60% of living cells in the 24 h and 48 h periods, however. A significant increase in apoptotic cells was observed after the photodynamic therapy treatments, for both 24 and 48 h groups. Over 50% of cells were under apoptosis after photodynamic therapy, evidencing a death process generated from the oxidative damage of the treatment. Comet assay and micronucleus assessments, both of which evaluate genotoxicity, demonstrated favorable results to damages caused by the photodynamic therapy treatment. Thus, photodynamic therapy is proposed to damage nuclear cells and the subcellular structure of carcinogenic cells. Impact statement Recently, the use of photodynamic therapy grows as an alternative treatment for cancer, since it has a noninvasive characteristic and affinity to the tumor tissue. Accordingly, understanding the therapy’s foci of action is important for the technique improvement. This work aims to understand the genotoxic effect triggered by the therapy action, thus evidencing the permanent changes caused to the genetic material of the tumor cell after the treatment. Therefore, to increase the knowledge in this study field, the methodology of the comet assay and count of micronucleus formed after the therapy was adopted in order to understand if the damage caused to the DNA of tumor cell makes its replication process unfeasible in future generations. The study allows a better therapeutic approach to the cancer treatment, making the process of association between therapies a more effective option during the disease treatment.