Hydroxyapatite (HAp) is a biomaterial with a large number of useful applications. In this work, a method for the preparation of HAp at nanoscale was developed (nano-HAp). The prepared nano-HAp was used in the extraction of methyl orange (MO) from water. The special chemical composition, the crystal structure of HAp and molecular structure of MO made extraction occurs at a good efficiency. Structure of the prepared HAp was confirmed by powder X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscope. Batch experiments were used to evaluate the tendency of the prepared nano-HAp for extracting the MO from water. The effect of temperature, time, pH and the amount of adsorbent on the rate of adsorption were evaluated and found to have a noticeable effect on the adsorption efficiency. The optimum conditions for extraction of MO by nano-HAp were determined. In all runs, in the first 5–15 min of contact time at room temperature the nano-HAp showed the highest rate of adsorption. Then, the rate leveled off after about 20 min. The temperature showed almost directly proportional with the rate of adsorption. The thermodynamic studies revealed a spontaneous nature of adsorption at different temperature. © 2017 Desalination Publications. All rights reserved.