The process of transcription initiation in eukaryotic cells is complex and our view of how the transcription apparatus is assembled at the promoter has changed over the last decade. For most genes transcribed by RNA polymerase II (Pol II) general transcription factors and Pol II assemble at the core promoter and initiate transcription at specific sites. The number of distinct core promoter elements is increasing and so is the number of specific proteins that act through these elements. Core promoter elements include the TATA box, TFIIB recognition element (BRE), the initiator (INR), and the downstream promoter element (DPE). Transcription factors that act through these elements are TATA binding protein (TBP) and its associated factors (TAFs), Negative Cofactor 2 (NC2), Mot1p, TFIIB, and TFIIA. Recent observations suggest that TBP, Mot1p, and NC2 exert positive and negative effects on transcription complex assembly depending on the presence or absence of specific core promoter elements. It is proposed here that Mot1p and NC2 together function as a remodeling complex that positions TFIID and perhaps other protein complexes at specific core promoter elements.