The diversity of MTOR-regulated mRNA translation remains unresolved. Whereas ribosome-profiling suggested that MTOR almost exclusively stimulates translation of TOP (terminal oligopyrimidine motif) and TOP-like mRNAs, polysome-profiling indicated that MTOR also modulates translation of mRNAs without 5 TOP motif (non-TOP mRNAs). We demonstrate that in ribosome-profiling studies detection of MTOR-dependent changes in non-TOP mRNA translation was obscured by low sensitivity and methodology biases. Transcription start site profiling using Nano-Cap Analysis of Gene Expression (nanoCAGE) revealed not only do many MTOR-sensitive mRNAs lack 5 TOP motif but that 5 UTR features distinguish two functionally, and translationally distinct subsets of MTOR-sensitive mRNAs: i) mRNAs with short 5 UTR enriched for mitochondrial functions, that require EIF4E, but are less EIF4A1-sensitive and ii) long 5 UTRs mRNAs encoding proliferation- and survival-promoting proteins, that are both EIF4E- and EIF4A1-sensitive. Selective inhibition of translation of mRNAs harboring long 5 UTRs via EIF4A1 suppression leads to sustained expression of proteins involved in respiration but concomitant loss of those protecting mitochondrial structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5 UTR mRNAs, by MTOR inhibitors, results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5 UTR features define different modes of MTOR-sensitive translation of functionally distinct subsets of mRNAs which may explain the diverse impact of MTOR and EIF4A inhibitors on neoplastic cells.