Seed potato certification aims to ensure the production of high-quality planting material while limiting the spread of pathogens. This is particularly necessary in potato production due to vegetative propagation, which facilitates the accumulation and transmission of diseases across generations. Among these, Potato virus Y (PVY) and Potato leafroll virus (PLRV) are of major concern, as they can be transmitted through the vascular system and by aphid vectors in non-persistent (PVY) and persistent (PLRV) manners. Other pathogens, including blackleg (Pectobacterium spp., Dickeya spp.) and late blight (Phytophthora infestans), are also monitored within certification schemes. In Switzerland, the sanitary status of seed potato lots is assessed through field inspections, laboratory analyses and post-control plots. Each multiplication plot is inspected two to three times during the growing season. Since 2016, annual molecular testing of PVY and PLRV has been conducted by RT-qPCR. Approximately 220,000 tubers from 1,000 lots are sampled each year, with an average of 10,000 RT-qPCR analyses performed. Data over the past decade indicate that PVY is the most prevalent virus, while PLRV incidence has increased since 2019. Co-infection by PVY and PLRV rose from an average of 6 % (2016–2018) to an average of 13% since 2019. Each year, the proportion of rejected seed potatoes lots varies, due not only to viral infections but also to blackleg and late blight, depending on weather conditions. These observations emphasize the importance of long-term monitoring to support effective seed potato certification and the deployment of disease control strategies.