Combinatorial auctions have been studied analytically for several years, but only limited experimental results are available for auctions with more than 10 items. We investigate the Hierarchical Package Bidding auction (HPB), the Combinatorial Clock auction (CC), and one pseudo-dual price auction (PDP) experimentally, as all these formats were used or suggested for high-stakes spectrum auctions. We want to understand the impact that different auction formats have on bidder behavior and allocative efficiency. Interestingly, we find that the main source of inefficiency in all formats is the bidders’ preselection of packages, rather than their strategies or auction rules; bidders mostly preselect a small number of packages of interest early in the auction. CC achieves high efficiency and revenue in all experiments, but HPB yields similar results even in value models, where hierarchical pre-packaging is difficult. Due to their influence on the decision of the US Federal Communications Commission, we intentionally repeated a set of experiments conducted by Goeree and Holt (GH) [Games and Economic Behavior 70:146–169, 2010], and find similar aggregate results. In addition, we analyze the CC auction and find that this mechanism has advantages in environments where the auctioneers’ hierarchy does not fit the bidders’ preferences well. In addition to the value models with global synergies in GH, we used value models where bidders have local synergies, which play a significant role in spectrum auctions in the field and lead to different results.