Objective: Describe the clinical and epidemiological characteristics of patients under 2 years of age hospitalized with whooping cough in a tertiary care children’s hospital in Peru. Methods: This was a case series of patients under 2 years of age who were hospitalized with a diagnosis of whooping cough in 2012. Results: A total of 121 patients were hospitalized. Diagnostic testing (direct immunofluorescence, polymerase chain reaction, culture) was carried out in 53.72% of patients. Overall, 23.15% (n = 28) were confirmed cases, all of whom were patients less than 10 months old, and none of whom had received 3 doses of whooping cough vaccine. A total of 96.43% (n = 27) of cases were under 6 months of age, 42.86% (n = 12) were younger than 3 months, and 10.71% (n = 3) were admitted to the intensive care unit. Of these cases, all were younger than 2 months old, and one patient died. The most common symptoms in the confirmed cases were coughing (96.43%), facial redness (96.43%), paroxysmal coughing (92.86%), and coughing-related cyanosis (78.57%). The most frequent probable epidemiological contact was the mother (17.86%), and the majority of cases occurred in the summer (46.43%). Conclusion: Whooping cough is a cause of morbidity and mortality, especially in those younger than 6 months of age and in those who are not immunized or only partially immunized. Vaccination rates should be improved and case confirmation encouraged to prevent the underdiagnosis of this disease.