Temporal pattern of lipids changes in stroke patients and its prognostic significance has not yet been fully understood. Our aim was to assess the early temporal changes of lipids in acute ischemic stroke patients and its prognostic significance in predicting stroke outcome. Total cholesterol, LDL-cholesterol, HDL-cholesterol and triglycerides were measured at admission, 24 hours, 48 hours, 72 hours, and at discharge. Stroke outcome was assessed by infarct volume, neurological deficit at discharge and 90 days stroke mortality. We have included only patients for whom blood and all clinical data were available at all time points during the follow-up period. In our stroke cohort (n = 52) there was a mean decrease of HDL-cholesterol from admission to discharge (0.32 mmol/L, 23%), accompanied with an increase in triglyceride concentration of 0.3 mmol/L (8%). LDL-cholesterol and total cholesterol had an initial rise at 24 hours, followed by the subsequent fall at 48 hours, 72 hours, and at discharge. Decreased HDL-cholesterol at 48 hours after stroke onset and at discharge is associated with poor patient functional outcome. Patients with large infarct volume had significantly higher concentrations of total cholesterol and LDL-cholesterol at 24 hours, 48 hours, and at discharge than patients with small and medium infarct volume. Early after the onset of acute ischemic stroke there is a marked change in the concentration of serum lipids. Reliable assessment of lipid status cannot be done during the early period after the stroke onset.