The present paper analyses both managerial and program efficiencies of Lithuanian family farms, in the tradition of Charnes et al. (Manag Sci 27(6):668–697, 1981) but with the important difference that multi-directional efficiency analysis rather than the traditional data envelopment analysis approach is used to estimate efficiency. This enables a consideration of input-specific efficiencies. The study shows clear differences between the efficiency scores on the different inputs as well as between the farm types of crop, livestock and mixed farms respectively. We furthermore find that crop farms have the highest program efficiency, but the lowest managerial efficiency and that the mixed farms have the lowest program efficiency (yet not the highest managerial efficiency).