Low potato productivity in Ecuador is partly attributed to the use of low quality seed tubers. However, seed health quality in Ecuador, and its interaction with altitude and yield has been poorly investigated. We surveyed 11 farmers fields in Ecuador in 2010 to determine incidence and severity of pathogens and pests affecting foliage and seed tubers, and to determine the influence of altitude and seed sources over seed health quality (pathogen and pest diversity in/on the seed tuber). Additionally, a field experiment was planted in CIP-Quito using assessed seed tubers collected from surveyed farmers fields, during 2010 and 2011, to determine yield responses to seed health quality. Results show that foliage was mainly affected by late blight and flea beetle damages while seed tubers were predominantly affected by black scurf, andean weevil damages, potato virus S and potato virus X. We found that seed health quality was similar among farmers seed sources, and detected that increase in altitude decreased seed-borne virus diversity. Only seed-borne pathogens and presence of mechanical damages were found to explain yield variation. Seed-borne pathogens affecting yield variation were black scurf on seed tubers, potato virus S, and potato yellow vein virus. However, these factors changed when regressions were performed per seed source or variety. The yield responses to seed health quality of each variety should be considered to fine-tune integrated pest management strategies.