Microspheres loaded with Indomethacin were prepared by employing ionotropic gelation by using sodium tri polyphosphate (Na-TPP) as the crosslinking agent. Chitosan microspheres produced by an emulsification crosslinking process with the chemical crosslinker, glutaraldehyde has problems associated with its use as it may cause toxic reactions and other undesirable effects. The FT-IR spectroscopic analysis indicated the absence of any drug-polymer interaction during the microsphere preparation. Surface morphology of the prepared microspheres was confirmed by Scanning Electron Microscopy (SEM). The prepared microspheres were subjected for evaluation of particle size distribution, drug loading and entrapment efficiency. The results of the in vitro drug release shows that with increase in the crosslinking density the rate of the drug release decreases. Indomethacin was present in the amorphous state and dispersed uniformly in the polymeric matrix of the microspheres as shown from the results of the XRD and DSC studies. From the preliminary studies, it can be concluded that the method developed and adopted for the preparation of drug loaded microspheres is simple and reproducible and also avoids the use of special precautions and complex apparatus.