Salmonella enterica is highly diverse in terms of genome structure, which is at least partly due to the horizontal transfer of genetic elements from various sources. In this study, we examined the expression profiles of such genes in $underline{S}$almonella $underline{P}$athogenicity $underline{I}$slands (SPIs) and the cob/pdu locus, horizontally acquired large DNA segments, during growth under standard growth conditions. Transcripts from exponentially growing and early stationary phase Salmonellae were compared using various methods including cDNA microarray analysis. Nearly all genes encoded by SPIs and the cob/pdu locus were induced at the onset of the stationary phase in a stringent molecule ppGpp-dependent but stationary phase ${sigma}$, ${sigma}$38-independent manner. Although, it has been suggested that ppGpp acts in concert with DksA, we found the stationary phase induction of those SPI genes was not DksA dependent. It is suggested that ppGpp stimulates the expression of these stress-inducible genes encoded by horizontally acquired DNA, by itself or in concert with DksA.