There is increased interest in using cell penetrating peptides such as HIV Tat-derived peptide (Tat) to deliver biologically active cargo to cells. However, little is known about the precise molecular mechanism in cells after the uptake of Tat and after it conjugates with the cargo. Using high-density microarray analysis, we evaluated the alteration of whole genomic responses in U-937 macrophages that had been treated with Tat and Tat-fluorescein-5-isothiocynate (FITC), which served as model cargo, and then incubated for 24 h. Sixteen genes were upregulated and 28 downregulated in Tat-treated cells. After FITC had conjugated to Tat, 13 genes were upregulated and 23 downregulated. Ten upregulated and 13 downregulated genes were overlapped by both Tat and Tat-FITC. The molecular functions of regulated genes affected by Tat and Tat-FITC are described. A real-time quantitative reverse transcriptase-polymerase chain reaction was used to confirm three regulated genes (IFNAR2, CASP8, and CRLF1) affected by both Tat and Tat-FITC. We demonstrated that regulating the three genes was time-dependent and that CASP8 is also kinetically regulated in HeLa cells. Understanding the influences and consequences of Tat (Tat-cargo)-induced gene changes should help us design and develop efficient and safe delivery systems into target cells.