Functional magnetic resonance imaging (fMRI) methods allow rapid and non-invasive determination of brain structure and brain function, characteristics that are of particular importance in studies involving children. The goal of analysis of fMRI time series is to extract the best estimate of neuronal activity from the recorded hemodynamic signal. This process is made difficult by a host of instrumental and physiologic artifacts encountered in fMRI data acquisition and analysis. Structural and functional brain imaging using commercial magnetic resonance (MR) imaging systems has an excellent safety record. fMRI has been employed clinically to study language function in children. One of the most important applications of pediatric fMRI studies lies in clinical studies. Clearly a number of limitations imposed by the MR environment need to be taken into consideration when conducting functional neuroimaging with MRI. The outcome of the statistical analysis is greatly determined by the acquisition parameters and experimental procedures.