Time-resolved hypocotyl length measurements in seedlings have the potential to greatly aid genetic studies looking at light, hormone, and circadian regulation of cell expansion. Recently, several computer-based tools have been developed to quantify hypocotyl length during photomorphogenesis and early seedling development. Here we detail a method for quantifying Arabidopsis seedling hypocotyls in an image-based assay, focusing on light-grown seedlings responding to shade conditions.