Few studies have investigated the prevalence of shaking and smothering and whether they are associated with co-sleeping. In Japan, co-sleeping is common during infancy and early childhood. This study investigates the prevalence of shaking and smothering and their associations with co-sleeping among 4-month-old infants in Japan. A questionnaire was administered to mothers who participated in a 4-month health checkup program in Kamagaya City in Japan (n = 1307; valid response rate, 82%). The questionnaire investigated the frequency of self-reported shaking and smothering during the past one month, co-sleeping status, and living arrangements with grandparents, in addition to traditional risk factors such as stress due to crying. Associations between co-sleeping and self-reported shaking or smothering were analyzed using multiple logistic regression. The prevalence of self-reported shaking and smothering at least one time during the past one month was 3.4% (95% confidence interval (CI), 2.4%-4.3%) and 2.4% (95% CI, 1.5%-3.2%), respectively. Co-sleeping was marginally associated with the amount of crying and not associated with stress due to crying. Further, co-sleeping was not associated with either self-reported shaking or smothering, although stress due to crying showed strong association with shaking and smothering. Co-sleeping was not a risk factor for shaking and smothering.