Background Previous studies find that both schizophrenia and mood disorder risk alleles contribute to adult anxiety and depression. Emotional problems (depression or anxiety) begin in childhood and show strong continuities into adult-life; this suggests that symptoms are the manifestation of the same underlying liability across different ages. However, other findings suggest there are developmental differences in the etiology of emotional problems at different ages. These include (a) differences in treatment responsiveness and gender ratios in child/adolescence compared to adulthood, (b) recent genetic findings that schizophrenia risk alleles were specifically associated with “earlier-onset” ( Methods Data were analyzed using regression-based analyses in two UK, prospective, population-based cohorts (NCDS and ALSPAC). Schizophrenia and Major Depressive Disorder (MDD) Polygenic Risk Scores (PRS), were derived from published Psychiatric Genomics Consortium genome-wide association studies. Emotional problems were assessed prospectively from age 7 to 44 years in NCDS and from age 7 to 18 years in ALSPAC. Results Schizophrenia PRS were associated with emotional problems from childhood (β=0.044, p=0.005) to mid-life (β=0.033, p=0.023), while MDD PRS were associated with emotional problems only in adulthood (β=0.035, p=0.011; childhood β=0.014, p=0.372). Associations between schizophrenia PRS and early emotional problems appear to be driven by anxiety rather than depression. Discussion Our prospective investigations suggests that early (childhood) emotional problems in the general population share more genetic risk with schizophrenia, while later (adult life) emotional problems also shared genetic risk with MDD. This is consistent with findings from cross-sectional clinical studies of MDD. The results suggest that the genetic architecture of depression/anxiety is not static across development.