The behavior and morphology of sex chromosomes pairing in spermatocytes of the brown rat have been studied by surface spreading, silver and phosphotungstic acid(PTA) staining techniques. The results are as follows. Sex chromosomes axial cores thicken before X and Y pairing. X Y pairing is delayed until early pachytene. The first pairing initiation site is located on telomere of the short arms of X and Y chromosomes. The second pairing initiation site is located on teltomere of the long arms of X and Y chromosomes or on the interstitial position of the long arms of X and Y. Pycnosis speed of sex axial cores is different with different stages during prophase I of meiosis. In middle Pachytene the almost whole Y is fully paired in SC association with about one-third the X. On the region of X-YSC, lateral elements of X-YSC divide into two skeins, bubble appears on one of the two skeins and the unpaired X and Y axial cores are in variable forms. X Y pairing initiation sites, relationship of X Y pairing and genetic homology and mechanism of thickening and variable X Y axial cores were discussed.