The objective of this study was to evaluate the impact of freezing on the lyophilization of a concentrated formulation with a high fill depth. A model system consisting of a 15-mL fill of 15% (w/w) sulfobutylether 7-beta-cyclodextrin (SBECD) solution in a 30-mL vial was selected for this study. Various freezing methods including single-step freezing, two-step freezing with a super-cooling holding, annealing, vacuum-induced freezing, changing ice habit using tert-butyl-alcohol (TBA), ice nucleation with silver iodide (AgI), as well as combinations of some of the methods, were used in the lyophilization of this model system. This work demonstrated that the freezing process had a significant impact on primary drying rate and product quality of a concentrated formulation with a high fill depth. Annealing, vacuum-induced freezing, and addition of either TBA or an ice nucleating agent (AgI) to the formulation accelerated the subsequent ice sublimation process. Two-step freezing or addition of TBA improved the product quality by eliminating vertical heterogeneity within the cake. The combination of two-step freezing in conjunction with an annealing step was shown to be a method of choice for freezing in the lyophilization of a product with a high fill depth. In addition to being an effective method of freezing, it is most applicable for scaling up. An alternative approach is to add a certain amount of TBA to the formulation, if the TBA-formulation interaction or regulatory concerns can be demonstrated as not being an issue. An evaluation of vial size performed in this study showed that although utilizing large-diameter vials to reduce the fill depth can greatly shorten the cycle time of a single batch, it will substantially decrease the product throughput in a large-scale freeze-dryer.