Family-genetic studies suggest that anxiety disorders run in families and that mechanisms of familial transmission might act as early as during pregnancy. The aims of the Maternal Anxiety in Relation to Infant Development (MARI) Study are to prospectively investigate the course of pregnancy in women with and without anxiety disorders prior to conception from early pregnancy to postpartum focussing on (a) maternal psychopathology, (b) maternal perinatal health, and (c) offspring outcomes that are supposed to be early indicators/ antecendents for later anxiety disorders. The MARI Study is a prospective-longitudinal study program with seven waves of assessment: T1 (baseline: week 10 to 12 of gestation), T2 (week 22 to 24 of gestation), T3 (week 35 to 37 of gestation), T4 (10 days postpartum), T5 (2 months postpartum), T6 (4 months postpartum), and T7 (16 months postpartum). Overall, N = 306 pregnant women were enrolled during early pregnancy (T1) and allocated to one of the following initial diagnostic groups: no AD: no anxiety nor depressive disorder prior to pregnancy (N = 109), pure D: pure depressive disorder(s) prior to pregnancy (N = 48), pure A: pure anxiety disorder(s) prior to pregnancy (N = 84), and comorbid AD: comorbid anxiety and depressive disorders prior to pregnancy (N = 65). Overall, N = 284 mothers could be retained until T6 (retention rate: 92.8 %) and N = 274 until T7 (retention rate: 89.5 %). Clinical and psychosocial measures were used including a standardized diagnostic interview (CIDI-V) with dimensional scales and standardized observation paradigms (mother-infant-relationship, infant temperament and neuropsychological development). Dimensional anxiety and depression liability indices were developed to reflect the severity of anxiety and depressive disorders prior to pregnancy and to ease longitudinal modelling. Findings from this study will contribute to improved knowledge about the natural course of anxiety disorders during transition to parenthood and associated outcomes that are assumed to be early indicators of later psychopathology in the offspring. Results are expected to provide new insights into mechanisms of familial transmission and clues for targeted prevention and early intervention.