The structure of alternating multilayers of two diacetylene group containing amphiphiles (an acid (A) and a pyridine ligand (B)), built up from a 5 mM CdBr2 subphase, is examined. SAXR measurements revealed that these multilayers have a regular layer structure with a bilayer spacing of 55.2 Angstrom. From this bilayer spacing in combination with FT-IR measurements, it can be concluded that the aliphatic tails of amphiphile A have a tilt angle (ct) of about 34 degrees with respect to the surface normal, while in the case of amphiphile B, alpha has a value of about 45 degrees. In the all-trans aliphatic alkyl chains of both amphiphiles, the C-C-C plane has a preferred orientation such that the symmetric stretches of the methylene groups of the aliphatic chain must be close to being in a plane parallel to the substrate. These multilayers can be partly polymerized by means of UV irradiation, forming the red form (lambda(max) = 540 nm) of the polymer. Upon polymerization the regular layer structure is preserved and the bilayer spacing increases from 55.2 up to 57.9 Angstrom. The preferred orientation of the C-C-C plane of the aliphatic tail chain around the chain director is lost during the polymerization process. Also, the all-trans alkyl chain is partly converted in a more irregular one containing gauche conformations.