Tea (Camellia sinensis (L). Kuntze) cultivation by smallholder out-growers has grown significantly. Recent government initiatives have expanded production from traditional tea growing regions. This study investigated how smallholder farmers perceive and prefer different commercial tea clones. It also looked at the factors that influence their choices across major tea-growing regions of Uganda. A structured questionnaire was administered to 324 randomly selected tea out-growers from Central, Western, Kigezi, and West Nile regions. Data was analyzed using descriptive statistics, a Tea Preference Index (rating clone attributes on a 1–5 scale), and a multivariate Probit (MVP) model to evaluate farmers’ choices and preferences. Clone 303/577 is the most cultivated, accounting for 59%. Adoption rates were high in West Nile (98%), Kigezi (77%), and Central (67%) regions. Clone 6/8 ranked second at 47%, while clone 100/5 had the lowest cultivation rate at 10%. The ranking of clones by preference was 303/577, 6/8, 108/82, 31/8, and 100/5. Key attributes influencing preferences included, yield potential, canopy width, post-plucking/pruning recovery rate, shoot tenderness and cup quality. Results showed that a farmers’ choice of clone 303/577 was significantly influenced by shoot density, gender and tea farming experience. For clone 108/82, the most important factors were quick recovery after plucking/pruning, education level and household size. This information is vital for agricultural policy, extension services, tea breeding and genetic improvement programs in the tea sector.