Pomegranate juice has been an erectile dysfunction miracle worker on the Peak Testosterone Forum and has rescued many guys from bedroom difficulties. What is particularly amazing is how it seems to really help some of the young guys out, who supposedly have clean arteries and should be without erectile issues. For example, check out what this young man recently wrote in:
“Pomegranate juice is the bomb. I’m 35 and was suffering from weak erections for about a year. I then read Peak’s articles on pomegranate juice, especially how it could possiblly reverse plaque buildup, and I figured I’d give it a whirl. Generally a 1/2 hour after consuming it I notice that I have no erection issues. Consuming 4-8 oz. before bed results in morning wood most mornings. This stuff has improved my relationship with my girlfriend, and it’s all natural! I was afraid that I would have to start taking Viagara.” 
And this is just one of probably a dozen guys that have written in and said how pomegranate juice has helped them dramatically. Of course, the temptation with anything that is so effective is to take a lot. Us guys will do just about anything to get back in the game, right? And the studies on pomegranate look very, very good: as I document in my page on The Benefits of Pomegranate Juice, it helps nearly every arterial parameter you can conceive of from lipids to inflammation to plaque, etc. It’s just a cardiovascular wonder worker.
However, you have to step back and ask yourself if something that powerful could actually cause some issues for some men potentially. For example, caffeine can be miracle worker as well, but in some men it can cause arrythmias and other issues. Although research is very preliminary, pomegranate juice may end up falling into this same category for some men, although I suspect the real issue will be dosage.
In any event, check out these studies for some potential concerns with Pomegranate Juice that are poorly understood and understudied. I currently consume pomegranate juice but have cut back my dose. My take on it is that pomegranates have been consumed heavily for hundreds of years, so I find it hard to believe that reasonable amounts of of pomegranate juice that correspond to a couple of pomegranates would cause major issues. But who knows? Again, look at these studies and do your own research:
1. Potential Damage to Neurons (a mock Parkinson’s)? One study on mice sought to verify Pomegranate’s protective effect in a mouse model of Parkinson’s Disease. Parkinson’s basically occurs when one loses too many of the dopamine-producing cells in the brain’s substantia nigra region (80-90%). Now Pomegranate has powerful antioxidant effects and, undoubtedly, for this reason it has shown some protective effects from Parkinson’s (in animal models).  However, pomegranate juice is also a potent stimulator of nitric oxide, a free radical. So, theoretically, any stimulator of nitric oxide could create too much NO and cause actual oxidative damage. This is exactly what a later study found and the researchers noted the following:
“The present study was assigned to examine the potential neuroprotective effects of PJ [pomegranate juice] in the rotenone model of PD [Parkinson’s Disease]. Oral administration of PJ did not mitigate or prevent experimental PD but instead increased nigrostriatal terminal depletion, DA neuron loss, the inflammatory response, and caspase activation, thereby heightening neurodegeneration.” 
So you have one study showing it may help with Parkinson’s and another that says it might worsen it. Again, I suspect it is a matter of dosage, but there is no doubt that more studywork and research needs to be done.
3. Interaction with Medications. Pomegranate juice can affect literally dozens of different medications – not just PDE5 Inhibitors. The reason is that it inhibits several of the liver’s cytochrome enzyme families. Check with your doctor first if you are on any medications. 
4. Mouth and Gum Issues. I know that after a few weeks of taking pomegranate juice, my mouth begins to develop sores. The tongue and gums will be painful to the touch and then I’ll quit pomegrante and the problem will go away within 48 hours. I have repeated this experiment several times, so I do not doubt that pomeranate is the root cause. And realize that pomegranate completely changes many oral (mouth) properties. (Yes, you have mouth flora just like you have gut (intestinal) flora and both are very important to your health.) One study considered thise changes to be positive and the researchers concluded that:
“The changes were: reduced total protein (which can correlate with plaque forming bacteria readings), reduced activities of aspartate aminotransferase (an indicator of cell injury), reduced alpha-glucosidase activity (a sucrose degrading enzyme), increased activities of the antioxidant enzyme ceruloplasmin (which could give better protection against oral oxidant stress) and increased radical scavenging capacity (though this increase was significant only by nonparametric statistical analysis). A placebo of cornstarch in water did not affect these measures. These data raise the possibility of using pomegranate extracts in oral health products such as toothpaste and mouthwashes.” 
So this sounds positive, but I cannot help but wonder if pomegranate is too powerful in some people, thus causing some oral issues in some men (like myself). And I am not the only one reporting this effect. Just do a search on “pomegranate mouth ulcers” or “pomegrante mouth sores” and you’ll see dozens of entries come up.
2) Neurobiology of Aging, May 2014, 35(5):1162 1176, “Pomegranate juice exacerbates oxidative stress and nigrostriatal degeneration in Parkinson’s disease”
3) Neurobiology of Disease December 2006, 24(3):506 515, “Pomegranate juice decreases amyloid load and improves behavior in a mouse model of Alzheimer’s disease”
4) Urol Ann, 2012 May-Aug, 4(2):108 110, “Priapism, pomegranate juice, and sildenafil: Is there a connection?”
5) DMD, February 2007, 35(2):302-305, “Effects of Pomegranate Juice on Human Cytochrome P450 2C9 and Tolbutamide Pharmacokinetics in Rats”
7) DMD, May 2005, 33(5):644-648, “EFFECTS OF POMEGRANATE JUICE ON HUMAN CYTOCHROME P450 3A (CYP3A) AND CARBAMAZEPINE PHARMACOKINETICS IN RATS”
7) Phytother Res. 2009 Aug;23(8):1123-7. doi: 10.1002/ptr.2759. Pomegranate extract mouth rinsing effects on saliva measures relevant to gingivitis risk.