As part of a national action plan to manage animal genetic resources in Burundi, we characterized smallholders’ goat production systems and assessed the effect of Boer crossbreeding on animal body measures. To that end, 319 farmers were surveyed in the five agro-ecological zones of Burundi and the zootechnical measures of 939 adult goats were taken. Cluster analysis of the goat production systems resulted into two opposed groups and one intermediate. On the one hand, there are the dry lowlands systems characterized by large herds composed mainly of indigenous animals grazing freely, and having high market characteristics. On the other hand, there are the humid highlands systems characterized by small herds composed of indigenous and crossbred animals in stall feeding or herding/tethering systems, and by low market characteristics. Fixed effect linear models were used to evaluate the effect of Boer crossbreeding on body weights and linear body measures, after adjustment for age, sex, grazing systems and agro-ecological zones. Results showed that least square means for body weights of adult Boer crossbreds were 4.74 kg higher than those of indigenous goats, which was lower than expected. Least square means for linear body measures of Boer crossbreds were significantly higher than those of indigenous breeds: differences in chest girth, body length and height at withers were 4.88 cm, 5.59 cm and 4.82 cm, respectively. Goats were heavier and greater in linear measures in lowlands than in highlands. The advantages and issues of a selection programme within indigenous breeds are discussed as an alternative to the crossbreeding programme.