Linear enamel hypoplasia (LEH) has been utilised in human bioarchaeology as an indicator of growth disturbance during childhood. However, only a few studies have compared populations of different socio‐economic status in the same time period. This study examines the association between the LEH occurrence pattern and social status in the 18th to 19th century populations in Japan. Detailed archaeological studies on burials from the Edo period (1603–1867) excavated in Tokyo have facilitated estimating an individual's social status by its burial type. In this study, 112 individuals from the Sugenji‐Shokenji site were divided into three burial structure groups (ceramic jar coffins for middle‐class warriors, wooden square coffins for low‐class warriors and townspeople and wooden circular coffins for townspeople) and examined for the general prevalence of LEH, number of LEH and the chronological distribution of LEH. A high general prevalence of LEH was observed in every group, especially in lower canine (79.3–100.0%). However, individuals in the jar coffin group showed a lower prevalence and smaller number of LEH per tooth, suggesting that individuals of higher social status experienced better living environments in their childhood. There was no significant difference in the chronological distribution of LEH formation between coffin groups. Such data are essential for understanding the association between socio‐economic status and living conditions in specific societies in the past. Copyright © 2015 John Wiley & Sons, Ltd.