Abstract In this work, it was developed a fast, simple and selective method for quantification of genipin and geniposide from unripe fruits of genipap, which are known as natural colorants, blue and yellow, respectively. The compounds separation was performed in a fused-core C18 column using as mobile phase water (A) and acetonitrile (B) both acidified with 0.1% formic acid, with the following gradient: 0 min, 99% A; 9 min, 75% A; 10 min, 99% A and 13 min, 99% A. The temperature and flow rate that allowed the best chromatographic performance were 35 °C and 1.5 mL/min, respectively, resulting a total run time of 13 min, including column clean-up and re-equilibration. This short analysis time represents an advantage compared to the methods reported in the literature where the running times are 2-5 times greater. The detection wavelength was set at 240 nm. The method validation was performed based on specificity, linearity, detection and quantification limits, precision and accuracy, according to ICH methodology. Finally, the developed method was suitable for monitoring analysis of those compounds content in vegetable samples.