The recently developed green laser (GL; wavelength 543 nm) is thought to measure perfusion derived from a more superficial skin layer than does the standard near-infrared laser (RL; wavelength 780 nm). These lasers were used to investigate the disturbances in the different layers of skin perfusion in ischaemic legs before and after treatment and compared with capillary microscopy. Eighteen patients (20 legs) with different stages of leg ischaemia scheduled for a vascular intervention (11 males, 7 females; median age 73, range: 52–81 years; Fontaine stages II–IV) were investigated by means of capillary microscopy, visualising the nail fold capillary perfusion, and a laser Doppler, equipped with a special dual probe conducting both GL and RL. The probe was attached to the pulp and the dorsum of the big toe to assess skin perfusion at rest and during reactive hyperaemia, while sitting and while supine. Resting and hyperaemic perfusion using GL was low and significantly lower (p < 0.01) than with RL in both areas and positions. Laser Doppler perfusion was higher in the pulp than on the dorsum with both wavelengths (p < 0.05). The hyperaemia response was highest using GL and differed among the three techniques. Postural reduction of capillary and RL flow was reduced, but not with GL. After treatment, skin capillary perfusion improved more clearly than did the laser Doppler perfusion with either wavelength, while postural vasoconstriction improved only when measured with the capillary microscope. The differences found between RL and GL Doppler perfusion, but also between GL and capillary microscopy measurements suggest that the GL does measure the more superficial, but not exclusively the nutritive skin perfusion. Clinically, the use of the green laser in its present form in patients with leg ischaemia offers no advantage over the red laser.