In this paper, hydroxyapatite (HA), flour-hydroxyapatite (FHA) and fluorapatite (FA) powders have been synthesized in nanometric scales by sol-gel method. Structural changes, morphology, phase analysis and in vitro behavior of powders were studied. According to the XRD and SAED results, increasing the fluorine precursor caused an increase in the degree of crystallinity and crystallite size. FT-IR results demonstrated the replacement of F-in OH-positions and formation of FHA or FA. SEM and zetasizer studies showed that increasing of fluorine amounts raised the aptitude for agglomeration. According to the direct measurement during TEM studies, the crystallite sizes were found to be between 20 and 50 nm. The samples with higher amounts of fluorapatite resulted in the increasing of cells counts in the fibroblast cell culture experiment. So, fluor ion has a positive effect on biocompatibility of FHA powders.