A two-stage approach is employed to analyze the efficiency of cooperatives responsible for ruminants’ disease control (OPP) at the farm level in Northwest Portugal. In the first stage, Data Envelopment Analysis (DEA) is used to estimate and decompose input-based overall inefficiency for each OPP. The input-based inefficiency measures are generated using the directional input distance function. In the second stage, the inefficiency estimates are regressed on environmental and organizational factors in order to explain efficiency differentials. Despite substantial environmental differences, the empirical results indicate that most cooperatives can reduce costs by improving scale efficiency and pure technical efficiency.