The aim of the present study was to prepare a colon targeted pellet formulation of secnidazole and to evaluate the formulation in vitro and in vivo by a gamma scintigraphy method. Pectin/ethyl cellulose in different ratios and in different coating labels with plasticizer was used to prepare secnidazole pellets by a powder layering technique. The formulations were tagged with 99mTC-DTPA, a tracer in gamma scintigraphy to evaluate its transit behavior in rabbits. Morphology and compatibility were studied using Scanning Electron Microscopy, IR spectroscopy and Differential Scanning Calorimetry were used for the characterization of prepared pellets. The in-vitro study suggested that pectin (59%) esterification and ethyl cellulose 45cps at 20% coating label led to an optimum bacterial enzyme dependent released behavior. The optimized formulation was subjected to an in-vivo transit study. Scintigraphy images clearly indicated that the formulation can delay the drug release prior to the colon. The average time of gastric emptying and colon arrival was 57 min and 6.08 h, respectively. The coated pellets prepared by powder layering technology successfully released drug in the colon indicating that site specificity has been achieved with pectin 59% esterification and ethyl cellulose 45 cps at 1:2 ratio with 20% coating label.