Various deoxycholic acid (DOCA) bearing heparin (HD) amphiphilic conjugates with different degrees of substitution (DS) with DOCA were synthesized using heparin as a hydrophilic segment and DOCA as a hydrophobic segment. Structural characteristics of these HD conjugates were investigated using 1H NMR, dynamic light scattering, zeta potential, transmission electron microscopy (TEM), and fluorescence spectroscopy. HD conjugates provided monodispersed self-aggregates in water, with mean diameters decreasing with increasing DOCA DS in the range of 120-200 nm. HD aggregates were covered with negatively charged heparin shells, exhibiting ξ potentials near -56 mV. The critical aggregation concentration (cac) of the HD (0.02-0.003 mg/mL) depended upon DOCA DS. TEM images demonstrated that the shape of the self-aggregates was spherical. Partition equilibrium constants, Kv, for pyrene in the self-aggregates in water indicated that increasing DS enhanced the hydrophobicity of the self-aggregate inner core. The mean aggregation number of DOCA per hydrophobic microdomain, estimated by the fluorescence quenching methods using cetylpyridinium chloride, indicated that five to nine of HD chains comprised a hydrophobic domain in the conjugates.