The crystal structures of three 3-halogeno derivatives of 13N-substituted cytisine have been determined by X-ray diffraction. The two 13-acetyl substituted compounds, 3-bromo (1) and 3-iodo (2) are isostructural, with the isostructurality index as high as 99%. They both crystallize in monoclinic P21 space group, with unit cell parameters of a = 8.4709(10) A, b = 9.2266(12) A, c = 8.6051(10) A, β = 98.528(11)o (1) and a = 8.2322(6) A, b = 9.1724(7) A, c = 8.5494(6) A, β = 98.181(7)o (2). In turn, 3-bromo-13-t-butyl-carbonate derivative (3) crystallizes in orthorhombic P212121 space group with a = 6.8171(3) A, b = 7.8994(4) A, c = 31.4657(15) A. Conformation of the cytisine skeleton is similar in all three molecules, with almost planar A ring, sofa conformation of B-ring and C ring being an almost ideal chair. However, the orientations of the double C=O bonds in 13N-substituents are completely different: in 1 and 2 it is cis with respect to C12 (C12-N13-C14-O15 torsion angle is 3.3(4)o in 1 and 1.3(6)o in 2) while in 3 it is trans (−175.4(3)o). In the structures of 1 and 2 the driving force of the crystal architecture are quite strong C–H···X halogen bonds with C···X distances far shorter than the sums of van der Waals radii (C···Br in 1 is 2.9430(19) A and C···I in 2 2.974(3)). In contrast in 3–partially as the consequence of different orientation of the substituent—there are no halogen bondings but instead some weak C–H···O contacts organize the molecules into two-dimensional patterns. In two 3-halogeno-N-acetyl cytosine derivatives the strong, directional halogen bonds influence the crystal packing, while for 3-bromo-N-t-butyl-carbonate derivative only weak hydrogen bonds are observed.