A detailed in situ study of silicide reactions during rapid thermal annealing of patterned structures was performed to determine the effects of linewidth (0.2 to 1.1 μm), dopants (arsenic, boron or phosphorus) and silicon substrate type (poly-Si or <100>-Si) on the C49 to C54-TiSi2 transformation. A synchrotron x-ray source and a high speed position sensitive detector were used to collect x-ray diffraction patterns of the reacting phases on a millisecond time scale, in situ, during annealing. We demonstrate that most patterned C49-TiSi2 structures (0.2 to 1.1 μm in width, 2 to 4 μm2 in area) will incompletely transform into C54-TiSi2 during rapid thermal annealing. The C49 to C54 transformation ends at about 900°C and further annealing to higher temperatures does not force the remaining C49 to transform into C54. We also observed that the C54 formation temperature increases as the linewidth of the silicide structure decreases. These results are explained by a low density of C54 nuclei in C49 which leads to a one-dimensional growth of C54 grains along the length of the patterned lines. Finally the incorporation of a Mo implant into either poly-Si or <100>-Si before the deposition of titanium is shown to increase the percentage of C49 that transforms into C54 and also to lower the C54 formation temperature.