The study examined the effect of farmers’ perception about the quality of seed yam typically used for cultivation on their preferences for certified seed yam. Heckman’s sample selectivity probit model was applied on survey data collected from 380 yam farmers. The study found that farmers generally agree that the use of certified seed yam would help to improve yield because of minimum to no disease/pest infestation. Farmers expressed their willingness to purchase certified seed yam if the price is about 26% higher than those supplied from the informal system in as much as the quality can be assured. The study found that farmer educational level, experience, access to extension services and household incomes were factors influencing farmers’ perception about quality of seed yam cultivated. Variables such as age, educational level and income were also found to be factors that influence farmers’ preference for certified seed yam. The results were similar for both Pona and other white yam varieties. The study recommends promotion of farmer education through increased access to extension services on seed quality assessment together with other agronomic practices including farmer field schools, to help improve their ability to assess the quality of seed yam obtained from other sources as well as increase their preference for certified seed yam.