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Based on potential high efficiency, low thermal budget and compatibility with very thin Si wafers, many research groups and industries are considering interdigitated all back contact silicon heterojunction (IBC-SHJ) solar cell technology. Compared to front junction silicon heterojunction (FJ-SHJ) solar cells, IBC-SHJ cells also have the unique advantages for simpler module integration. However, the IBC-SHJ solar cells to date suffer with low fill factors. Both simulation and experimental results have been conducted to understand the cause of the low FF. In this paper, the effects of processing conditions are discussed by comparing FJ-SHJ and IBC-SHJ solar cells. The fabrication of IBC-SHJ cells requires several photolithography steps to form the interdigitated back structure, whereas the FJ-SHJ requires no photolithography steps. The effect of processing temperatures, deposition sequence and photolithography processing are evaluated by using the FJ-SHJ as a test bed and base-line standard. Contamination and/or introduction of defects at intrinsic/doped layer interfaces resulting from photolithography steps is identified as one of the major contributors to reduced performance of IBC-SHJ devices fabricated using a low temperature process.