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The last decade has seen a reappraisal of the process of agricultural innovation and a convergence on participatory approaches to development planning and research. Recognizing that practitioners face scarcity of information on how to operationalize the new paradigm, the project reported here aimed to develop a methodology for integrating scientific soil survey products with indigenous knowledge surveys. In principle, these methods offer complementary strengths. Scientific survey provides valuable insight into key soil properties and their spatial variability, but such mapping is generally not available at sufficiently detailed scale. On the other hand, indigenous knowledge is fine-tuned to locality and represents an assembly of accumulated local experience. Field research over 3 years on sites in Uganda and Tanzania aimed to test the hypothesis that indigenous knowledge and scientific soil assessment can both be represented within a common spatial frame and can therefore be usefully integrated. The research highlighted the importance of a systematic and iterative exploration of indigenous knowledge, which must extend beyond the level of rapid rural appraisal and include several different techniques of cross-validation of interpretations of indigenous soil classification systems. We conclude that there is much to be gained by combining elements of broad-scale scientific survey with a localized assessment of indigenous knowledge. The remaining challenge is to develop best practice guidelines that will allow agricultural researchers and planners to understand and use local knowledge combined with scientific understanding of soil and land resources.