In this paper we consider a Bayesian treatment of ‘Duhem's thesis’, the proposition that theories are never refuted on empirical grounds because they cannot be tested in isolation from auxiliary hypotheses about initial conditions or the operation of scientific instruments. Sawyer, Beed, and Sankey (1997) consider Duhem's thesis (and its restatement in stronger and weaker forms as the ‘Duhem-Quine thesis’) and its role in hypothesis testing, using four theories from economics and finance as examples. Here we consider Duhem's thesis in the context of theory choice, econometric results, and the ‘farm problem’ in agricultural economics. This problem is defined as persistently low and highly variable prices, incomes, and returns in the agricultural sector as compared to the nonagricultural sector of the U.S. economy. The existence of the farm problem tends to refute an implication of general equilibrium (GE) theory — that resources flow to equate returns between sectors of the economy. We discuss Duhem's thesis in the context of demonstrating why evidence supporting the farm problem has not diminished the standing of general equilibrium theory among agricultural economists.