Nucleotide compositional analyses of disparities in genomic guanine and cytosine (gGC) content directly relate to the amino acid composition, through the union of the genetic code. Here we analyzed 229 prokaryotic genomes to address the intricate relationships between gGC, amino acids and their codons in the context of genes. First, we not only confirmed the universal rule that the average GC content at codon position 1 (GC1) is always higher than that at codon position 2 (GC2), but also extended the rule to show that it holds true even when codon-position-related GC contents are calculated on a per gene basis. The "GC1>GC2 rule" is attributable essentially to a few dominant amino acids that have GC at one of these two codon positions or the intermediate-GC group of amino acids. Second, we found that gGC fluctuations were largely compensated for at the codon level, when codons belonging to high-GC and low-GC amino acid groups varied accordingly. Finally, we found that prokaryotic genes also have a GC content gradient (Gd) distributed along their transcripts. The gradients at three codon positions (Gd1, Gd2 and Gd3) all correlated with gGC in two different directions: Gd3 was positive, whereas the other two were negative.