This paper addresses the efficiency assessment of production units in cases where some characteristics of the production process are known. In particular we focus on the existence of direct linkages between inputs and outputs, where certain outputs are produced from specific inputs and not jointly produced from all inputs. Our aim is to use and empirically compare alternative forms of reflecting the linkages between inputs and outputs. The alternatives to be compared to reflect the linkages between inputs and outputs are: the use of separate assessments; the use of ratios between linked outputs and inputs; and the use of differences between linked outputs and inputs. These alternatives are presented and contextualised within existing procedures for dealing with output-specific inputs, and results are discussed and illustrated empirically in the context of evaluating Portuguese courts’ efficiency.