In this paper, we propose a new way of thinking about molecular self-organization of the antibiotic amphotericin B (AmB) by examination of its N-iodoacetyl derivative (AmB-I). This choice was dictated by the simplicity of AmB-I crystallization as compared to pure AmB. The studies focus on spectroscopic investigations of the monocrystal and the amorphous state of AmB-I. The results of vibrational, FTIR, and Raman spectroscopy show differences between the crystalline and amorphous forms, in particular for bands attributed to C=O (1700-1730 cm(-1)) and C-C-H groups, as well as C=C-C (ca. 1010 cm(-1)) stretching vibrations. The process of crystallization is identified by strong differences in the intensities and locations of these characteristic bands. For the AmB-I crystals, the carbonyl band is shifted toward lower frequencies as a result of intensified hydrogen bonding in the crystalline form. Detailed analysis indicates that bands in the region characteristic for the C=C-C bending distortion in the chromophore are particularly intense for AmB-I in the crystalline form as compared to the intensity of this band in the amorphous state. These findings are corroborated by the results of fluorescence spectroscopy. We observe a much faster decay of the emission for the AmB-I monocrystal as compared to the DMSO solution of AmB-I. Interestingly, the fluorescence decay in the amorphous form requires three decay times for simulating the observed behavior; two of these decay constants are sufficient for estimating the decay measured for the AmB-I crystals. The proof of the molecular organization of AmB-I molecules is obtained from polarization-resolved fluorescence spectroscopy on a single AmB-I crystal. Strong anisotropy of the emission intensity correlates with the axes of the crystal, providing insight into actual alignment of the molecules in the AmB-I crystals. These findings related to molecular organization in AmB-I crystals are crucial for understanding toxicity mechanisms of the clinically used drug, amphotericin B.