There is little known about real world psychopharmacological prescribing practices in managing pregnant women with severe mental illness (SMI). This study utilised a sample of 535 women with a SMI across two hospitals in Australia. This included women with psychotic disorders, bipolar disorder and a range of non-psychotic disorders. The majority of women with a SMI in pregnancy were prescribed psychotropic medication as part of their management. Furthermore, more than one class of agent was prescribed for 31% of women with psychotic disorders and 30% of women with bipolar disorder. Differences between sites were identified in prescribing practices across the mental disorders. This included the variation in rates of use of multiple agents and pattern of use across pregnancy. This study also identified that women with a SMI had elevated rates of gestational hypertension, gestational diabetes mellitus, smoking and obesity in pregnancy and neonates admitted following delivery compared with the Australian average. These findings suggest that studies that examine associated risks for severe mental disorders or their treatments on pregnancy and infant outcomes should take into account the prescribing practices including the likelihood of exposure to polypharmacy and a range of potential confounding co-morbidities and exposures. The discrepancies in reported findings for pregnancy and infant outcomes following use of antipsychotic and mood stabiliser agents such as lithium may be at least partially accounted for by the complexity of multiple exposures that includes use of multiple psychopharmacological agents, co-exposures such as smoking and co-morbid conditions such as obesity.