Ion chromatography was used to determine the inositol content in formula foods for special medical purposes. The sample was acidified by hydrochloric acid to precipitate proteins, and inositol was dissolved in the supernatant and then detected with an amperometric detector. The results showed that the peak area was linearly related to the concentration of inositol in the range of 0.025 to 40.000 mg/L with a correlation coefficient (R2) of 0.999 9. The detection limit and quantitation limit were 0.125 and 0.5 mg/100 g, respectively. The average recovery of inositol was 83.1%–102.9% at different spiked levels. The method was proved to be simple, sensitive reproducible and suitable for the determination of inositol in formula foods for special medical purposes.