Laser irradiation has proved to be very efficient in speeding and improving the quality of healing in pathological conditions of diverse etiologies. However, the mechanisms by which the beneficial effects are attained are not clear. Mitochondria are the primary phototargets during irradiation. The study aimed to establish if laser irradiation had an effect on hypoxic and acidotic cells. The study also aimed to use existing information regarding the possible mechanism of action (established in wounded cells) and apply these principles to acidic and hypoxic irradiated cells to determine whether laser has a stimulatory or inhibitory effect. Cell cultures were modified to simulate conditions of hypoxia (hypoxic gas mixture 95% N2 and 5% O2) and acidosis (pH 6.7) whereas the central scratch model was used to simulate a wound. Cells were irradiated with a helium–neon (632.8 nm, 3 mW cm−2) laser using 5 or 16 J cm−2 on days 1 and 4. Mitochondrial responses were measured 1 or 24 h after laser irradiation by assessing changes in mitochondrial membrane potential (MMP), cyclic AMP, intracellular Ca2+ and adenosine triphosphate (ATP) cell viability. Hypoxia and acidosis significantly reduced MMP when compared with normal nonirradiated control cells. Wounded, hypoxic and acidotic cells irradiated with 5 J cm−2 showed an increase in mitochondrial responses when compared with nonirradiated cells while 16 J cm−2 showed a significant decrease. The study confirmed that laser irradiation with 5 J cm−2 stimulated an increase in intracellular Ca2+ which resulted in an increase in MMP, ATP and cAMP, which ultimately results in photobiomodulation to restore homeostasis of injured cells.