L-arginine and taurine are still in the center of physiological and pharmacological research. Although the fate of nitrogen of both compounds and of the 35S-taurine is well-documented, the fate of the carbon skeleton has not been elucidated yet. We studied the organ distribution of 14C arginine and 14C taurine over time in the mouse using whole body autoradiography with densitometric image analysis. We describe different organ distribution patterns. Kidney, heart, lung, the Harderian gland, the central nervous system, intestine and testis showed a comparable pattern of arginine disappearance in contrast to rapid disappearance in the salivary gland and the accumulation pattern in bone and spleen. Data on 14C taurine of liver, kidneys, lung, testis and Harderian gland resembled the arginine pattern; Accumulation of taurine carbon was found in salivary gland, bone, intestine, heart and brain. Our studies challenge and demand further related studies to obtaining more information on the fate of the carbon skeleton of these amino acids.