Proteins of fifty or fewer amino acids are poorly characterized in all organisms. The corresponding genes are challenging to reliably annotate, and it is difficult to purify and characterize the small protein products. Due to these technical limitations, little is known about the abundance of small proteins, not to mention their biological functions. To begin to characterize these small proteins in Escherichia coli, we assayed their accumulation under a variety of growth conditions and after exposure to stress. We found that many small proteins accumulate under specific growth conditions or are stress induced. For some genes, the observed changes in protein levels were consistent with known transcriptional regulation, such as ArcA activation of the operons encoding yccB and ybgT. However we also identified novel regulation, such as Zur repression of ykgMO, CRP repression of azuC, and CRP activation of ykgR. The levels of eleven small proteins increase after heat shock and induction of at least one of these, YobF, occurs at a post-transcriptional level. These results show that small proteins are an overlooked subset of stress response proteins in E. coli, and provide information that will be valuable for determining the functions of these proteins.