It depends how the phrase is used. Someone could be using the term "male reproductive organ" as a politer way of referring to the penis. The penis and testicles are the main parts of the male reproductive system.
The testes (or testicles) create sperm cells. One epididymis is located on the back of each testis and acts as a ripening chamber for the sperm cells. From there, the sperm cells travel up the right or left vas deferens to the seminal vesicles, where they are stored and mixed with other fluid. The prostate gland and the bulbourethral gland also secrete fluids into the seminal vesicles. These additional fluids help nourish the sperm cells and make them more motile. The seminal vesicles also connect to the urethra, the tube used for carrying urine from the urinary bladder to outside the body. There is a band of muscles called a sphincter where the seminal vesicles attach to the urethra. They allow the seminal vesicles to build pressure to be able to shoot the semen out of the penis during ejaculation. Ejaculation is when the male reaches climax (orgasm) during sex and ejects semen.
From a reproductive system standpoint, the semen is intended to enter the woman's vagina, travel up through her uterus, and make its way to the fallopian tubes, where it might find an egg cell to fertilize. The fertilized egg then travels to the uterus and implants itself. Then perhaps 9 months later, the woman delivers a baby.
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The Urethra is the passage for urine to leave the body. It is located in the Penis.