Many children experience pre-school or early childhood wheezing. In a significant proportion symptoms disappear as the child grows, but others have persistent and troublesome asthma which can be life-long. Tools to predict course of disease in young children are a priority for families and clinicians. This review summarizes evidence from several longitudinal population-based birth-cohort studies that have identified risk factors for persistence and remission of childhood asthma. These factors include clinical characteristics, environmental and other exposures, familial factors, biomarkers of allergic inflammation, measurements of lung function and airway responsiveness, and genetic variants. This review also introduces the concept of polygenic risk and genetic risk scores, and describes results from a recent study that suggests promise for the use of genetic information in predicting the course of childhood asthma. We conclude with a discussion of implications and future directions.