The DNA polarity, i.e. the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states. Here we examine this aspect for two dinucleotides containing adenine and guanine: 5'-dApdG-3' and 5'-dGpdA-3' in water. We used two different femtosecond transient absorption setups, one providing high temporal resolution and broad spectral coverage (330-650 nm) between 30 fs and 50 ps, the other recording decays at selected wavelengths till 1.2 ns. The transient absorption spectra corresponding to the minima in the potential energy surface of the first excited state were computed by quantum chemistry methods. Our results show that the excited charge transfer state in 5'-dGpdA-3' is formed with a quantum yield 75% higher and slower decay (170±10 ps vs 112±12 ps) compared to 5'-dApdG-3'.