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We investigate gender differences in agricultural productivity in Nigeria and Uganda. Results indicate persistent lower productivity on female-owned plots and among female-headed households, accounting for a range of socio-economic variables, agricultural inputs and crop choices using multivariate tobit models. Results are robust to inclusion of household-level unobservables and alternative specifications that account for decisions to plant crops. However, productivity differences depend on aggregation of gender indicator, crop-specific samples, agro-ecological zone and biophysical characteristics. More nuanced gender data collection and analysis are encouraged to identify interventions that will increase productivity and program effectiveness for male and female farmers.