This study aimed to assess the potential risk factors for lower respiratory tract infection (LRTI)-related hospital admissions in Mongolian children. A population-based cross-sectional study was conducted in rural Mongolia in 2013, and 1,013 mother-child pairs were included. Of the participating children, 38.9% were admitted to hospital with LRTIs. Home smoking, low birthweight, being a male child, exclusive breastfeeding and healthcare-seeking behaviour showed substantial association with LRTI-related hospital admissions. Number of cigarettes smoked by family members showed a dose-response relationship and increased hospital admissions. Strategies to prevent second-hand-smoke exposure from adult smokers, especially inside the home, are crucial to preventing LRTI-related hospital admissions for children in Mongolia. Improving rates of exclusive breastfeeding and increasing birthweight have great potential to decrease the likelihood of children acquiring a LRTI. Educational initiatives are also necessary for women who are less likely to seek out care for their children's symptoms.