Virus diseases are one of the most important factors affecting potato production worldwide, especially in developing countries, where only a small minority of potato farmers has access to certified seeds. The continued use of uncertified tuber-seeds can result in poor crop harvests as a consequence of seed degeneration, which is caused by the accumulation of pathogens and pests after successive cycles of vegetative propagation. In this study we evaluated the incidence of four RNA viruses (PVY, PLRV, PYVV and PVS) in both informal and commercial tuber-seeds marketed in the province of Antioquia (Colombia) using RT-qPCR. Viruses were detected in tuber-sprouts and their corresponding four-week-old plantlets. The presence of these viruses in commercial potato fields was confirmed by Sanger and High-throughput (HTS). Results revealed that commercial tuber-seed lots have a high incidence of PVY (81.7%), PYVV (70.0 %), PVS (30.0%) and PLRV (11.7%). No statistically significant differences were found in the levels of viral infection between informal and commercial tuber-seeds. HTS analyses of bulked leaf-samples revealed a high abundance of PVY and PVS, which ranked as the 2nd (10,047 TPM) and 24th (2,761 TPM) most abundant transcripts. This work reveal urgent need to update current potato seed-certification programs in Colombia.