Onychomycosis is the most common cause of nail changes accounting for about half of all nail diseases. It is important to diagnose the fungal pathogen to prescribe adequate treatment, but as genus- and species-specific diagnostic tests can be time consuming and expensive, it is crucial to obtain representative tissue during nail scrapings. Optical coherence tomography (OCT) is a non-invasive imaging tool enabling real-time imaging of skin and tissue. Pilot studies using OCT have described morphological characteristics of onychomycosis, though diagnostic criteria of onychomycosis and other nail diseases are lacking. The aim of this study is to investigate the applicability of OCT to detect and localize fungal elements in nails with clinical signs of onychomycosis. OCT scans and nail scrapings were performed on all participants and only confirmed cases of onychomycosis were included in the data analysis. All scans were analyzed, and a set of morphological criteria based on known literature and deviations from healthy nail morphology were suggested. The suggested morphological features were: hyperreflective lines divided into sharply and diffusely demarcated; hyperreflective dots divided into singular and clustered patterns; irregular surface, divided into mild, moderate and severe degree; dark bands and disturbed architecture. The suggested OCT morphology is a refinement of previous studies, and though OCT cannot replace genus- or species-specific identification, it could be a useful assistance tool to increase diagnostic sensitivity of nail scrapings and laboratory tests as well as for monitoring treatment response.