In therapy of port wine stain (PWS) birthmarks using pulsed green or yellow lasers, non-specific absorption by epidermal melanin reduces the amount of incident radiation that reaches the target PWS blood vessels. The related epidermal heating can induce blistering, dyspigmentation, or scarring, which limits the applicable radiant exposure, thus adversely affecting the efficacy of treatment in many patients. Our objective was to assess temperature depth profiles induced in PWS skin by a novel Nd:YAG laser emitting simultaneously at 1064 and 532 nm. The results should help determine safe radiant exposures for use in future clinical trials. The underlying hypothesis is that the added 1064 nm radiation may lead to a higher temperature increase in PWS relative to the epidermis, in comparison with a customary KTP/Nd:YAG laser system for vascular treatments (emitting at 532 nm only). The laser induced temperature profiles were determined in vivo using pulsed photothermal radiometry. A PWS test site was irradiated with a sub-therapeutic laser pulse and the transient change of the infrared radiant emission was recorded by a fast infrared camera. The laser-induced temperature profiles were reconstructed by solving the thermal-radiative inverse problem using an iterative minimization algorithm.