Second-generation antipsychotics (SGAs) are increasingly being used to treat children for a range of mental health conditions, for example, anxiety disorder, attention deficit hyperactivity disorder and bipolar disorder. SGA treatment is associated with weight gain and cardiometabolic side effects such as dyslipidemia, insulin resistance and elevated blood pressure, in some, but not all children. This review provides an overview of the potential role of pharmacogenomics in predisposing a child to unhealthy weight gain and cardiometabolic side effects with SGA treatment. Specifically, the review includes a synopsis of the evidence for cardiometabolic side effects in SGA-treated children, illustrating the extent and depth of the problem; summarizes the potential long-term consequences of developing cardiometabolic risk during childhood and highlights genetic variants that may be useful in predicting cardiometabolic side effects in SGA-treated children.