This study aimed to evaluate the potential of applying pectin and chitosan polysaccharides in pellet formulation. These biopolymers have advantages such as biocompatibility, low toxicity, low price and easy processing which make them interesting candidates for drug delivery purposes. Careful control of pellet porosity is essential to achieve an appropriate drug release profile. Replacing microcrystalline cellulose (MCC) with polysaccharides, especially pectin, leads to increased pellet porosity. Theophylline, dimenhydrinate and ibuprofen were chosen as model drugs. Investigation of possible ionic interactions between drugs and excipients is crucial to optimize the formulation of pellets with acceptable drug release. Differential scanning calorimetry of chitosan showed an endothermic peak; however, this peak was not observed in thermograms of the pectin, implying the lack of interaction between polysaccharides. Fourier transform infrared analysis did not indicate any interaction between drugs and polymers. Incorporation of MCC into the pellet formulation significantly increased the mean dissolution time while substitution of MCC with polysaccharides led to a faster release for each of the three drugs – that were different in their net charges – in both acidic and buffer media. These results highlight the potential value of polysaccharides in improving drug delivery characteristics of pharmaceutical pellets.