We studied the expression mRNA of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-2 (PFKFB-2) in the rat lung and kidney in experimental diabetes mellitus. For investigation we select two isoforms of PFKFB-2 with different C-terminus. The level of the expression of both PFKFB-2 mRNA isoforms is decreased in the kidney and lung in rats with experimental diabetes mellitus respect to the control animals. Moreover, four new alternative splice variants of PFKFB-2 mRNA were identified in the rat kidney. These splice variants of PFKFB-2 mRNA have different inserts and/or deletions in 6-phosphofructo-2-kinase as well as in fructose-2,6-bisphosphatase part of PFKFB-2. Three alternative splice variants cannot encode active 6-phosphofructo-2-kinase as a result of deletion of two catalytic domains (E and F). They encode fructose-2,6-bisphosphatase. It was shown that these alternative splice variants express in the kidney and lung and that this expression changes in rats with experimental diabetes mellitus with respect to the control animals. The results of this investigation clearly demonstrated that diabetes mellitus significantly affects the expression and alternative splicing of PFKFB-2 in the kidney and lungs and showed the complexity of regulatory mechanisms of glucose metabolism in this disease.