The recent shift of emphasis to on-farm conservation is driven by its diverse attractive features - participatory nature, dynamic nature, capacity to maintain not only crop diversity but the knowledge that evolves with it, the chance it offers and the challenge it brings to link conservation with farmers' livelihood. To make it operational, placing incentives and removal of perverse incentives are of critical importance. However, before placing sound incentives compatible to farmers' circumstances, the opportunity costs farmers face when using local varieties of public interest should be understood. This paper empirically examines farmers' opportunity costs of maintaining local varieties of sorghum using a household survey data collected from 198 sorghum growers in Eastern Ethiopia. Opportunity costs are generated using different homogeneous treatment statistical models and factors affecting them are further examined using switching regression model. The average opportunity costs suggest not only the size of policy incentive required for farmers to maintain local varieties of sorghum on-farm but also are useful to estimate the national costs of conserving crop genetic resources. The regression analysis shows that opportunity costs increase with access to output markets and extension, output price, access to input supply, experience in growing improved varieties, and relative importance of the crop. On the contrary, plot quality, input price and oxen ownership are reducing opportunity costs. The paper then concludes outlining the policy implications of the empirical findings to incentive design for on-farm conservation of crop genetic resources.