Microparticles containing isoniazid were prepared by the emulsification internal ionic gelation method using a novel, alkaline extracted ispaghula husk as a wall forming material. A four-factor three-level Box-Behnken design was employed to study the effect of independent variables on dependent variables. Sodium alginate concentration (X(1)), alkaline extraction of ispaghula husk (AEISP) concentration (X(2)), concentration of cross-linking agents (X(3)) and stirring speed (X(4)) were four independent variables considered in the preparation of microparticles, while the particle size (Y(1)) and entrapment efficiency (Y(2)) were dependent variables. Optimized microparticles exhibited 83.43% drug entrapment and 51.53 µm particle size with 97.80% and 96.37% validity, respectively, at the following conditions - sodium alginate (3.55% w/v), alkaline extracted ispaghula husk (3.60% w/v), cross-linker concentration (7.82% w/v) and stirring speed (1200 rpm). The optimized formulation showed controlled drug release for more than 12 h by following Higuchi kinetics via non-Fickian diffusion. The gamma scintigraphy of the optimized formulation in Wistar rats showed that microparticles could be observed in the intestinal lumen after 1 h and were detectable in the intestine up to 12 h, with decreased percentage of radioactivity (t(1/2) of (99m)Tc 4-5 h).