Background Accurate assessment of tumour size is important when planning treatment of nonmelanoma skin cancer (NMSC). Imaging with optical coherence tomography (OCT) has the potential to diagnose and measure depth of NMSC. Objectives To compare accuracy of mean tumour thickness measurement in NMSC tumours < 2 mm of depth using OCT and 20-MHz high-frequency ultrasound (HFUS). In addition, OCT morphology of NMSC was studied in OCT images and the influence of histological and colorimetric values on the quality and penetration depth in OCT images was estimated. Methods In total, 93 patients were scanned and 34 lesions [23 basal cell carcinoma (BCC) and 11 actinic keratosis (AK) lesions] < 2 mm thick and easily identified in OCT images were studied. OCT and HFUS were compared with biopsies. The influence of skin pigmentation and infiltration analgesia on OCT image quality was studied. Skin colour was measured with a colorimeter. Results OCT presented narrower limits of agreement than HFUS. Both methods overestimated thickness but OCT was significantly less biased (0·392 mm vs. 0·713 mm). No relation between OCT penetration depth and skin colour was found. Conclusions OCT appears more precise and less biased than HFUS for thickness measurement in AK and BCC lesions < 2 mm, but both OCT and especially HFUS tended to overestimate tumour thickness.