Short-chain fatty acids (SCFAs) are major products of the microbial fermentation of dietary fiber in the colon. Recent studies suggest that these products of microbial metabolism in the gut act as signaling molecules, influence host energy homeostasis and play major immunological roles. In the present study, defined the long-term effects of ceftriaxone administration on the fecal SCFAs concentration in Wistar rats. Ceftriaxone (300 mg/kg, i.m.) was administered daily for 14 days. Rats were euthanized in 1, 15 and 56 days after ceftriaxone withdrawal. Caecal weight and fecal concentration of SCFAs by gas chromatography were measured. Ceftriaxone administration induced time-dependent rats’ caecal enlargement through accumulation of undigestable substances. In 1 day after ceftriaxone withdrawal, the concentrations of acetic, propionic, butyric acids and total SCFAs were decreased 2.9-, 13.8-, 8.5-, 4.8-fold (P < 0.05), respectively. Concentration of valeric, isovaleric and caproic acids was below the detectable level. That was accompanied by decreased 4.3-fold anaerobic index and increased the relative amount of acetic acid (P < 0.05). In 56 days, concentration of SCFAs was still below control value but higher than in 1 day (except propionic acid). Anaerobic index was lower 1.3-fold (P < 0.05) vs. control. Conclusion: antibiotic therapy induced long-term disturbance in colonic microbiota metabolic activity.