Stochastic programming is used to model short-term uncertainty in long-term energy models of Scandinavia. Considering uncertainty in variables like wind power, hydropower and heat demand leads to significantly different results than deterministic models. Stochastic models show lower investments in wind power and higher investments in flexible electricity heating. It is important to evaluate solutions using methods like stability tests and sample average approximation to ensure high quality representations of uncertainty. Accounting for short-term uncertainty provides more robust insights from long-term energy models.