The nonequivalent groups with anchor test (NEAT) design involves missing data that are missing by design. Three equating methods that can be used with a NEAT design are the frequency estimation equipercentile equating method, the chain equipercentile equating method, and the item-response-theory observed-score-equating method. We suggest an approach to perform a fair comparison of the three methods. The approach is then applied to compare the three equating methods using three data sets from operational tests. For each data set, we examine how the three equating methods perform when the missing data satisfy the assumptions made by only one of these equating methods. The chain equipercentile equating method is somewhat more satisfactory overall than the other methods.