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Introduction: Despite the reported cases of whooping cough in Armenia, there has been no formal evaluation of “who these cases are and their load on hospital wards”. In a tertiary reference hospital, we determined the trend in hospitalized pertussis cases stratified by vaccination status and risk factors associated with apnea and hospital stay. Methodology: Retrospective cohort study of children (< 18 years) with confirmed pertussis hospitalized at the Republican Infectious Diseases Hospital between 2014 and 2018. Multivariate logistic regression was used to identify risk factors. Results: The majority (62%) of 116 children (44% female, mean age 21 months) were from regions outside the capital city of Yerevan. Standardized pertussis admissions increased by almost fivefold, from 2.2/1,000 in 2014 to 10.6/1,000 in 2018. The cumulative average percentage (2014-2018) of children not vaccinated against pertussis was 33%, while 29% were completely vaccinated. Twenty-five children (21%) had apnea, two of whom died. Younger age (Odds Ratio (OR) = 1.04; P = 0.05), not having been vaccinated (OR = 3.57; P = 0.01) and having comorbidities (OR = 4.1; P = 0.09) were associated with apnea. After adjusting for age, the longer hospital stay (>8 days) was significantly associated with non-vaccination (OR = 5.0, P = 0.002). Conclusions: There is a progressive increase in rate of hospital admissions for pertussis meriting closer vigilance on a national scale. Unvaccinated children of younger age are predisposed to apnea and longer hospitalization and would benefit from early referral to specialized infectious units. This may improve clinical outcomes and reduce hospital burden.