Seedlings sourced through tree nurseries are expected to form an important component of future tree cover on farms. As such, the genetic composition of nursery seedlings is expected to impact on the productivity and sustainability of agroforestry ecosystems. By surveying current practices of nursery managers in five areas from Kenya, Tanzania and Uganda, we quantified parameters associated with the collection, production and distribution of tree germplasm in East Africa. Considerable variation for seed-propagated nursery species was observed in the number of maternal parents (mother trees) sampled to establish nursery lots, the quantity of seedlings raised in nursery lots and the projected number of clients for nursery lots. Current seed collection practice was the most obvious limiting bottleneck in delivering high levels of genetic diversity to farmers. In the 143 cases analysed, seed to establish nursery lots was collected from a mean of only 6.4 maternal parents. In 22% of cases, ursery lots were established from a single maternal parent. On average, each maternal parent produced sufficient progeny to provide all the seedlings received by an individual nursery client. Consequently, the potential impact on farm and landscape genetic diversity of possible non-randomisation of progeny within nurseries is serious. In two instances, pair-wise analysis of transformed data suggested significant differences between geographic areas in the projected number of clients for nursery lots. We discuss improved nursery practices likely to promote genetic diversity, in particular increased maternal parent sampling and germplasm exchange.