The aim of this study was to compare aqueous dispersion and organic solution of Eudragit RS in preparation of sustained release theophylline microparticles using spray drying technique. Spray dried samples (SD) with drug:polymer (D:P) ratios of 1:1, 1:2, 1:3 were prepared using aqueous dispersion (SDaq) or organic solutions of Eudragit RS in ethanol (SDor). Properties of spray dried samples including yield, particle morphology, size distribution and drug dissolution were examined. Differential scanning calorimetry (DSC) and FTIR studies were performed to track any polymorphic changes in drug and/or drug- polymer interaction respectively. The SD samples were compacted and the crushing strengths and release profiles of tablets were determined. The yields of samples were in the range of 33-74%. The yield was higher for SDaq samples, being higher at higher D:P ratios. The SDor samples were smaller in size. SEM images confirmed the formation of spherical particles with somehow different structures for SDaq or SDor samples. Tablets prepared from SDor samples exhibited the highest crushing strengths. In study on release profiles for uncompacted samples, SDor samples exhibited superior sustained release properties. The same results were observed for compacted SD samples. DSC studies showed no polymorphism in SD samples and FTIR analysis showed that there was not any interaction between drug and polymer. In conclusion spray dried samples prepared from organic solution of Eudragit RS had superior sustained release properties and have more potential for application in sustained release formulation of theophylline than aqueous dispersion of the polymer.