The interfacial interaction and effect of biopolymer on crystal structure of hydroxyapatite in biomimetically synthesized nanocomposites, chitosan/hydroxyapatite (ChiHAP50), polygalacturonic acid/hydroxyapatite (PgAHAP50), and chitosan/polygalacturonic acid/hydroxyapatite (ChiPgAHAP50) have been investigated using atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy, and Rietveld analysis. AFM phase images show nano-sized hydroxyapatite particles uniformly distributed in biopolymer. FTIR spectra indicate that chitosan interacts with hydroxyapatite through NH(3)(+) groups, whereas in polygalacturonic acid/hydroxyapatite, dissociated carboxylate groups (COO(-)) form unidentate chelate with calcium atoms. A change in lattice parameters of hydroxyapatite in all nanocomposites is observed using Rietveld analysis. The increase in lattice parameters was most prominent along c-axis in ChiHAP50 and ChiPgAHAP50 nanocomposites, which was 0.388% and 0.319%, respectively. Comparison between particle sizes of hydroxyapatite, determined from AFM and Rietveld analysis, indicates presence of amorphous phase in hydroxyapatite particles, which is believed to be present at the interface of hydroxyapatite and biopolymer.