A system and method for measuring and analyzing motility within a body lumen such as the gastrointestinal (GI) tract, where an in vivo imaging device such as a capsule captures images and transmits the images to a processor, which calculates the motility of the device based on comparison of the images. Preferably, the processor compares the intensity of pairs of images or of elements of pairs of images, generates a variance for the compared images, and calculates the motility of the imaging device from the variances. The motility data may be presented to a user in various manners; for example, a plot of motility over time may be generated, or indications of low motility may be presented to the user of the system.