The purpose of the present study was to clarify the characteristics of fatal child maltreatment in families with multiple births in Japan. An exhaustive information search was performed to find multiple-birth cases between July 2003 and March 2011. There were 437 cases of fatal maltreatment of children aged 0–17 years during this period, including 14 involving multiple-birth children. A keyword search was performed to create a full profile for each multiple-birth case. The 14 multiple-birth victims were twins from 13 families. No significant difference between twins and singletons with fatal maltreatment was observed for most characteristics. However, in the case of twins, 0-month victims were rare, and the number of children per family was larger. One twin died from shaken baby syndrome. The victim's siblings were also maltreated in six out of 12 relevant cases, including all six co-twins. Premature birth, having a disabled co-twin, delay of growth or development, and parental disfavor tended to be factors of maltreatment when only one twin was maltreated. Four families were given suspended sentences in total, including three mothers who acted as solitary murderers (43% = 3/7). In conclusion, recent Japanese nationwide data suggests that the non-specific overburden of child rearing might be one possible reason for higher frequency of child maltreatment for multiples compared with singletons, and parental comparisons between two twins might be another. The penal sentences for fatal child maltreatment might be more lenient for perpetrators of this crime against twins than against singletons.