Optical coherence tomography (OCT) is a noninvasive, high-speed, and label-free imaging technique, providing 2D and 3D depth-resolved structures of biological tissue. In this study, we utilized a portable OCT system for in vivo studies of skin diseases and the evaluation of laser treatment outcome. A handheld probe with a light weight of 210 g is implemented for scanning arbitrary skin locations. To acquire en-face images at various skin depths, a segmentation algorithm was developed to identify skin surface and the boundary between the epidermis and dermis layers. According to the segmentation algorithm, skin parameters can be estimated including the thickness of stratum corneum, the thickness of epidermis, pore/hair follicle diameter, collagen concentration, and skin roughness. Moreover, the OCT images and skin parameters are used for clinical studies of skin diseases such as rosacea and psoriasis. In addition, the proposed method is utilized for observation and evaluation of laser treatment outcome in vivo. The results illustrate that such a portable OCT system could be potential for clinical diagnoses of skin diseases and laser treatment.