Whether a pulsed laser is superior to a continuous wave (CW) light source in photodynamic therapy (PDT) of cancer is still unclear and contradictory in the literature. Although photosaturation of a sensitizer and oxygen depletion in tumor have been considered to be involved during pulsed laser irradiation, there is a lack of experimental data. In the present work several parameters such as the amount of merocyanine 540 (MC540) in cells, the oxygen concentration in cells, and the amount of photos reaching cells during pulsed laser irradiation, were studied to compare the MC540-mediated PDT effects of a pulsed laser and a CW light source on murine myeloid WEH-3B (JCS) cells in vitro. The results showed that the pulsed laser was less effective at cell inactivation than the CW light under the same irradiation dose. However, when the energy of the pulsed laser was reduced from 0.25 to 0.06 mJ/cm2 while keeping the total irradiation dose unchanged, the photoinactivation of cells was increased significantly. Based on the measurements and calculations for the present experimental conditions, each cell has about 108 MC540 molecules bound (5 microg/ml MC540 for 1 hr) and receives about 109 photos from 0.25 mJ/cm2 of the pulsed laser. The results indicate that the photosaturation of MC540 occurs in the present conditions due to the fact that the photons received by one cell in one laser pulse were much more than the numbers of MC540 molecules bound to one cell. Thus, the photosaturation of the photosensitizer is one of the reasons to explain the different efficiency in cell inactivation between the pulsed laser and CW light.