Fully sequenced prokaryotic genomes ofEscherichia coli, Haemophilus influenzae andMethanococcus janaschii were subjected .to genome analysis for nucleotide interactions. The analysis was restricted to inter-nucleotide relations like two nucleotides in a dinucleotide, three nucleotides in a codon and two codons in a dicon. This relational analysis was carried out in C language and was compiled on a C++ compiler. The relational analysis showed a preferential dinucleotide frequency (the observed frequencies of AA and TT were higher than the expected frequency and the observed frequencies of CC and GG). From codon frequency distribution analysis, sub-codonic elements have been noticed, exerting that the first one or first two nucleotide may reasonably determine the next nucleotide(s) in a codon. The analysis further reveals the existence of short-range randomness or chaotic behaviour in prokaryotic genomes, which might be a forerunner for the origin of introns in eukaryotes, besides being involved in a regulatory role.