The feasibility of bispectral imaging photoplethysmography (iPPG) system for clinical assessment of cutaneous microcirculation at two different depths is proposed. The iPPG system has been developed and evaluated for in vivo conditions during various tests: (1) topical application of vasodilatory liniment on the skin, (2) skin local heating, (3) arterial occlusion, and (4) regional anesthesia. The device has been validated by the measurements of a laser Doppler imager (LDI) as a reference. The hardware comprises four bispectral light sources (530 and 810 nm) for uniform illumination of skin, video camera, and the control unit for triggering of the system. The PPG signals were calculated and the changes of perfusion index (PI) were obtained during the tests. The results showed convincing correlations for PI obtained by iPPG530 nm and LDI at (1) topical liniment (r = 0.98) and (2) heating (r = 0.98) tests. The topical liniment and local heating tests revealed good selectivity of the system for superficial microcirculation monitoring. It is confirmed that the iPPG system could be used for assessment of cutaneous perfusion at two different depths, morphologically and functionally different vascular networks, and thus utilized in clinics as a cost-effective alternative to the LDI.