Background: There are no population statistics collected on a routine basis on the children of prisoners in Australia. Accordingly, their potential vulnerability to adverse outcomes remains unclear. This study draws on linked administrative data to describe the exposure of children aged less than 2 years to maternal imprisonment in Western Australia, their contact with child protection services, and infant mortality rates. Results: In Western Australia, 36.5 per 1000 Indigenous (n = 804) and 1.3 per 1000 non-Indigenous (n = 395) children born between 2001 and 2011 had mothers imprisoned after birth to age 2 years. One-third of infants’ mothers had multiple imprisonments (maximum of 11). Nearly half (46%) of prison stays were for ≤2 weeks, 12% were between 2 and 4 weeks, 14% were for 1–3 months, and 28% were longer than three months. Additionally, 17.4 per 1000 Indigenous (n = 383) and 0.5 per 1000 non-Indigenous (n = 150) children had mothers imprisoned during pregnancy. Half of the children with a history of maternal incarceration in pregnancy to age 2 years came into contact with child protection services by their second birthday, with 31% of Indigenous and 35% of non-Indigenous children entering out-of-home care. Rates of placement in care were significantly higher for Indigenous children (Relative Risk (RR) 27.30; 95%CI 19.19 to 38.84; p <.001) and for non-Indigenous children (RR 110.10; 95%CI 61.70 to 196.49; p <.001) with a history of maternal imprisonment compared to children of mothers with no corrections record. Infant mortality for children whose mothers were imprisoned up to 5 years before birth or within their first year after birth was higher than for children of mothers with no corrections record for both Indigenous (RR 2.36; 95%CI 1.41 to 3.95; p =.001) and non-Indigenous children (RR 2.28; 95%CI 0.75 to 6.97; p =.147). Conclusions: This study highlights the particular vulnerability of children whose mothers have been incarcerated and the importance of considering their needs within corrective services policies and procedures. Prison may present an opportunity to identify and work with vulnerable families to help improve outcomes for children as well as mothers.