Renal uptake of a 35S labeled 18-mer phosphorothioate oligodeoxynucleotide (molecular wt approximately 6,000) was evaluated following intravenous infusion into rats. The kidneys contained 21 +/- 3% of the infused dose at five hours after infusion and 3 +/- 1% of the infused dose at four days after infusion. The concentration of oligonucleotide was greater in the kidney than in the liver, spleen, or plasma at both intervals. Urine excretion of oligonucleotide label averaged 17 +/- 1%, 35 +/- 5%, and 64 +/- 3% of the infused dose at five hours, one day, and four days after infusion. Electrophoresis (PAGE) showed that oligonucleotide was retained in the kidney was the intact 18-mer at both five hours and four days after infusion, while full size oligonucleotide was not found in the urine at either interval. Light microscopic autoradiography showed that oligonucleotide uptake was most prominent in the early proximal tubule. Electron microscopic autoradiography indicated that oligonucleotide was not confined to the brush border or endocytic-lysosomal pathway. Micropuncture studies showed that the tubule fluid to plasma concentration ratios of oligonucleotide label averaged 7 +/- 3% in Bowman's space and 6 +/- 2% in the distal tubule. Despite restriction of filtration by plasma protein binding, as indicated by the low Bowman's space to plasma concentration ratio, the calculated tubular reabsorption rate for oligonucleotide was sufficient to account for the large amount of oligonucleotide found in the kidney after intravenous infusion. These results indicate that the proximal tubule plays a prominent role in the disposition of intravenously infused oligonucleotide, and raise the possibility that oligonucleotides could exert antisense effects in this nephron segment.