The epididymis in the male reproductive tract is the site where spermatozoa produced from the testis become mature. The epididymis is divided into 4 different segments, initial segment and caput, corpus, and caudal epididymis, depending upon functional and morphological features. Aquaporins (Aqps) are water channel molecules, which are present in the epididymis and play a major role in removal of epididymal water, resulting in creation of microenvironment for sperm maturation and concentration of sperms. Nandrolone decanoate (ND) is a synthetic anabolic-androgenic steroid, which is used to treat clinical diseases and improve physical ability and appearance. Even though it is well determined that the ND causes the male infertility by affecting the testis, little is known the effect of the ND on the epididymis. The present study was focused to examine the effect of ND at different treatment doses and periods on expression of Aqp1 and Aqp9 genes in the epididymis of pubertal rats. Results showed that mRNA expression of Aqp1 and Aqp9 genes among the parts of the epididymis was differentially regulated by ND treatment doses. In addition, treatment periods of ND caused differential expression of Aqp1 and Aqp9 mRNAs among segments of the epididymis. Therefore, it is believed that male infertility induced by ND could be resulted not only from malfunction of the testis but also from aberrant gene expression of Aqp1 and Aqp9 in the epididymis.