Introduction: Cotton rats are a suitable model for the study of influenza disease symptoms and responses to influenza vaccination. We have previously shown that two immunizations with 15 µg whole inactivated virus (WIV) influenza vaccine could completely protect animals from infection with the H1N1pdm09 virus. Methods: To further explore the cotton rat model, we here investigated the protective potential of a single intramuscular immunization and of prime/boost intramuscular immunizations with a low amount of antigen. Results: A single intramuscular immunization with doses more than or equal to 0.5 µg WIV reliably evoked antibody responses and doses more than or equal to 1 µg protected the animals from virus replication in the lungs and from severe weight loss. However, clinical symptoms like an increased respiration rate were still apparent. Administration of a booster dose significantly increased the humoral immune responses but did not or only moderately improved protection from clinical symptoms. Conclusion: Our data suggest that complete and partial protection by influenza vaccines can be mimicked in cotton rats by using specific vaccination regimens.