The TAF N-terminal domain (TAND) of TAF1 includes two subdomains, TAND1 and TAND2, which bind to the concave and convex surfaces of TBP, respectively. Previous studies showed that the substitution of yeast TAND1 or TAND2 with the equivalent domain from a Drosophila homologue leads to accumulation of truncated Taf1p in yeast. This study demonstrates that these truncated Taf1p derivatives lack TAND. However, full-length Taf1p and untruncated derivatives are produced in yeast when several Met-to-Ala mutations are introduced in the carboxy-terminus of TAND. In contrast, mutations that reduce expression of full-length TAF1 do not reduce the amount of truncated Taf1p derivatives that are produced. These data suggest that TAND-deficient TAF1 derivatives are produced by initiating translation at alternative initiation sites. In addition, the TAF1 mRNA structure suggests that the TAND-deficient TAF1 derivatives may also be formed in yeast by use of (cryptic) alternative transcription initiation sites. Importantly, TAND-deficient truncated Taf1p appears to be produced at a low level in wild-type yeast as well. Finally, this study also demonstrates that Drosophila TAND2 substitutes functionally for yeast TAND2, but Drosophila TAND1 does not substitute for yeast TAND1.