Gastrointestinal (GI) motility is a key component of digestive health, and it is a complex both rhythmic and arrhythmic process governed by many physiological factors. The ability to accurately track the movements of the GI tissues in vitro over multiple days would provide valuable insights into GI tract physiology. A correlational analysis tracking algorithm was developed and applied to intestinal smooth muscle tissues that were maintained in organotypic culture. Physiologically relevant metrics, such as frequency, amplitude and motility index were independently assayed to quantify smooth muscle contractions. The results were validated by manually detected frequency determined using a standard software package. The algorithm was capable of tracking the changes in contractions of the same tissues over six days. This proof-of-concept study demonstrates the feasibility of long-term tracking of GI motility in organotypic cultures over multiple days. The approach allows study of the effects on GI smooth muscle contractility of direct controlled targeting of the cells and molecules in the GI tunica muscularis.