The relationship between variations in in vitro microbial biomass production and microbial protein supply to the host animal was examined in 13 Malawian goats fed on stover leaves from two varieties of maize at Bunda College, Malawi, in 1995. The in vitro parameters were analysed based on the concept of the partitioning factor (PF) which is obtained by the combination of gas volume measurements with determinations of the amount of substrate truly degraded. The PF reflects substrate-dependent variation in the in vitro partitioning of degraded substrate between short chain fatty acids (SCFA), gases and microbial biomass. The in vivo microbial protein synthesis was estimated by the urinary excretion of the purine derivatives (PD) allantoin, uric acid and xanthine + hypoxanthine. For the two types of stover leaves examined, the higher microbial efficiency of one variety in vitro was reflected by different PD excretions on practically identical digestible dry matter intakes in vivo. It is concluded that substrate-dependent variations in microbial efficiencies as detected by the PF are also evident and relevant for in vivo microbial protein synthesis.