This book constitutes the refereed proceedings of the Second International Workshop on Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data, STIA 2012, held in conjunction with MICCAI 2012 in Nice, France, in October 2012. The 13 papers presented in this volume were carefully reviewed and selected from 22 submissions. They are organized in topical sections named: longitudinal registration and transport; spatio-temporal analysis for shapes; spatio-temporal analysis under appearance changes; and spatio-temporal analysis for biology.