To answer Harry’s question about natural hormones, yes they would be more readily degraded, the rough general rule is that bacteria have a harder time breaking larger more complex molecules. My concern about hormones isnt so much about the plants taking it up, its more about the soil life, worms and insects etc that ultimately end up in the chickens and their eggs that supply my family.

I’m a pharmacist by trade(hence the interest in biochemistry) and have a love of sustainability. I practice permaculture myself, but I’ve simply identified some concerns i would have in my previous response with contaminants in urine. Personally i refrain from taking medicines unless required, but it’s also part of my profession to understand that many people require pharmaceutical help and that its not feasible to avoid them altogether.

My system at home includes chickens and quite a few ponds with many types of aquatic life. Any pharmaceutical presence will be directly relayed back to my family via the chickens and also contaminate the ponds and treasured native frogs. This is an important point for those interested in aquaponics. Amphibians and fish are a very sensitive lot, and Harry you are correct about organophosphates, medicines arent exclusively the only lot affect them. I would come to the conclusion that the use of urine in food crops is best for the undeveloped world where pharmaceutical intrusion is at a minimum.

Disease management is not a problem; storage times of 1-6 months will kill all pathogens. For a deeper analysis, see the Practical Guidance on the Use of Urine in Crop Production (1.6mb PDF) linked at the bottom of the article.

If the collection and treatment is occurring in the developed world on an industrial scale, it would be treated for pharmaceuticals during the storage phase. If it is occurring in the developed world at the home scale, the residual in the urine from medication could be an issue. I would wager the plants won’t actively take in the bad chemicals as long as the soil is fertile, if the buildup from a single family would even be enough to warrant concern.

In the developed world, you are right there is very little concern for medical contamination at either the industrial or family level. Again, disease management is a very small concern at both the family level, where you are more likely to spread disease person to person, and on the industrial level, where long storage times assure total pathogen destruction.

Pros:
-In the less developed world where people are less likely to have access to prescription medicines, the use of urine can be justified (however disease management becomes the priority).
- Indeed the use of urine closes the NPK loop, and where possible we should really return the fertility back to the fields provided that fertility doesn’t harbour long term contaminants.

Cons:
- Due to medical confidentiality, some people will prefer to keep their medical conditions private even with family members, and they are entitled to. This presents the problem that you will never know whether the urine is truly clean of pharmaceuticals.
- No guest is going to surrender their private ailments and medication list to their host, and so there’s another complication if they need to use the household bathroom.
- The use of urine as fertiliser is probably less feasible in the developed world due to these reasons. If its use is insisted on, then perhaps including it in hot composting can reduce the risks. Both heat and microbial degradation will help to reduce soil contamination. Risk management is ultimately up to the individual.

*Reference: MICROBIOLOGY 4th Edition- Prescott, Harley, Klein.