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Why Coffee is Bad for Me, but Might be Good for You

morning coffee

You know what I would like to do right now?

Drink a cup of coffee (an Americano from La Colombe to be exact).

Then have another.

After that, I’d bring the ship home with a few decaf Americanos (decaf has just as much caffeic and chlorogenic acid, the two most potent antioxidants in coffee, as does regular).1

So, yes, I love coffee. I love the ritual of coffee, the taste and the smell.

But here’s the thing.

Coffee, especially a daily caffeinated coffee habit, is not a healthy habit for me.


The bottom line is people respond differently to caffeine based in part on which version of a gene called CYP1A2 they carry.2 Your CYP1A2 status determines how fast your body will clear the caffeine you drink, and I carry a “slow” version of the gene.

When we drink caffeine, enzymes in the body break it down and get it out of our system. Some of us are fast metabolizers of caffeine, others like myself are slow metabolizers. The speed with which we break down caffeine determines the half life of the drug in our system. The half life of a drug like caffeine is the amount of time the drug is active before it is fully metabolized by the body. Since I carry the variant of the CYP1A2 gene associated with slower caffeine clearance, caffeine has a much bigger impact on me than it might on someone who carries a different variant of the gene.

In the standard western diet, coffee, which is chock full of polyphenols, is actually one of the primary sources of antioxidants for many Americans.3 And drinking coffee in moderation can be very healthy. I am definitely not here to hate on coffee, in fact my plan right now is to cycle on and off caffeine by building a couple coffee days into my week. Before I get into the weeds of why too much coffee is a bad look for many of us based on our genotype, let’s give coffee some love and list a few of the benefits.

Why coffee might be good for you

Perfomance Enhancer

We don’t need studies to tell us that caffeine is an obvious performance enhancer and a powerful nootropic, but of course the studies have been done.4 Drinking caffeinated coffee will help you get more stuff done and get it done better. Many people who are into nootropics claim “stacking” coffee with L-theanine makes it even better.

Mood Booster

This is a big one for me and the reason why I still have a few days a week that are “coffee days.” Drinking coffee makes me happy and social above and beyond my normal levels. I become chattier, more productive, etc. It’s great. My issue, which I will get more into in a minute, is the sleep deficit caffeine causes, which creates a definite law of diminishing returns as the weeks go on starting each morning with a few cups of Joe.

Lowers Uric Acid

The evidence is conflicting here, but there are some studies concluding that coffee intake can lower uric acid levels and help stave off gout.5 Of course, there are also studies which show the exact opposite.6 Although it may seem like an obscure metric to some, I include the uric acid issue on my list of benefits because anecdotally, I have found that espresso makes my urine more alkaline, and alkaline urine is associated with a greater ability to excrete uric acid. Even if you’re not in the gout range, uric acid is a particularly important biomarker in today’s high sugar world because many physicians think of it as a marker for fructose bio-toxicity. Lots of people who don’t have gout would actually find they had hyperuricemia (elevated uric acid) if they had their labs done. Uric acid blocks the synthesis of nitric oxide, which is the good stuff that causes blood vessels to dilate.

Healthy for the Liver

Coffee, both regular and decaf, is good for the liver. In fact, studies have consistently shown that drinking coffee helps bring down markers of liver inflammation and damage like alanine aminotransferase (ALT).7

Benefits for Heart Health

One of the latest studies to look at caffeine consumption, genetics and the risk of heart disease found no increased risk for CYP1A2 genotypes when consuming moderate amounts of coffee. In fact, the authors found that drinking moderate amounts of coffee was probably good for your heart. But be warned, they do say that drinking more than 5-6 cups of coffee per day is probably a bad idea and might play a role in increasing your risk for heart disease by as much as 22 percent, whatever that means. One thing I find funny about the study is setting the upper limit of 5-6 cups as “healthy.” That’s a ton of caffeine! Depending on strength of the coffee, 5 cups in a day is close to, or above, 1 gram of caffeine, which has been described in the medical literature as the threshold when very severe side effects can develop.

To quote this old paper published by the military:

Extreme side effects were observed in humans at caffeine intakes of 1 g (15 mg/kg) (Gilman et al., 1990), including restlessness, nervousness, and irritability, and progressing to delirium, emesis, neuromuscular tremors, and convulsions. Other symptoms included tachycardia and increased respiration.

This new study from the American Journal of Clinical Nutrition represents a departure from some others which found that high caffeine consumption and CYP1A2 do not mix. These studies found an increased risk of myocardial infarction (heart attack) and high blood pressure in slow metabolizers of caffeine.89

May Prevent Cognitive Decline

I am not sure how reliable they are as they are largely based on food frequency questionnaires, but there are studies out there which tend to show that drinking coffee (and to a lesser extent tea) in mid-life is associated with a 65% reduction in developing Alzheimer’s disease later in life. The theorized mechanism is greater insulin sensitivity.10

But, here’s the thing: poor sleep has also been linked to an increase in the plaques that damage the brain leading to Alzheimer’s.11 So, if you’re not getting good sleep because of poor caffeine metabolism, it’s definitely not a good idea to rely on population data as you drowsily poor yourself another cup of coffee to stay awake.

If coffee is bad for you, it’s bad for you. It doesn’t matter what a large scale study says.

Why Coffee is Bad for Me

By extension, you could really just substitute the word coffee for caffeine, but since coffee is my preferred delivery mechanism for my daily, or now weekly, caffeine dosing, I am just sticking with the coffee title here.

Coffee and CYP1A2

Ok, back to the genetics. We have a bunch of studies that have looked at how caffeine impacts slow metabolizers and the results haven’t been too pretty, especially as the number of cups mount each day (as they tend to do when we inevitably get addicted).

I cited the increased risk for heart attack and high blood pressure above, but for me the big issue is sleep.

Coffee blocks sleep

Think of this: we know caffeine has a half life, usually of about 5-6 hours, but this number varies a great deal based on genetics.

I am a slow metabolizer, so let’s say my morning cup of coffee has a half life of 7-9 hours. So, I have a 2 cups in the morning, then a decaf or two later in the day. When I want to get sleep later that night, the caffeine is still very active in my system. Why?

Because it’s not just the half life, caffeine has a quarter life, meaning it’s still has its hooks in you long after that morning sip. According to sleep scientist Matthew Walker, author of Why We Sleep, caffeine’s quarter life is about double its half life. This means that slow metabolizers like me may still be feeling the effects of our morning coffee well into the night. No wonder caffeine has been shown to be so disruptive of sleep.13 After all, it binds to and blocks our adenosine receptors, the signaling pathways the body uses to fall asleep each night.

Granted, one morning coffee may not be packing enough of a punch to keep most (some?) people awake all night, but that’s not what we are talking about, we are talking about disrupted sleep patterns. By far, the biggest issue for me when it comes to caffeine consumption is sleep. I get that amazing buzz the first few mornings, but as the days and weeks drag on, I need to drink more coffee to get the old results, and I end up using caffeine to mask symptoms of fatigue. Rather than a fun activity that gives my brain a boost, caffeine becomes a necessary input just to function normally. As I get less and less sleep, I want more caffeine, and on the cycle goes until I both look like and feel like shit.

So, in a nutshell, caffeine is bad for me because I process it very slowly. When I have a few cups of coffee and the quarter life is factored in, I could still be feeling the impact of that coffee in the wee hours of the night.

Caffeine is an addictive drug

And boy do I get addicted. I dip my toe in the water with one cup of decaf. By the end of the week I am at two espressos a day. A few weeks later I am thinking about a third cup, I start dreaming of my morning coffee as I am going to bed the night before. You get the idea.

Oh, and as I have written about in the past, caffeine withdrawal is real. If I try to quit, as I am doing now with a 7 day caffeine detox, the first few days are rough.


Although I find this problem to lessen as I drink more coffee, the euphoria of a morning coffee inevitably gives way to that “tweaked” anxious feeling by mid-afternoon. Heart racing a bit, uneasy, distracted, that type of thing. Focus becomes difficult. This doesn’t happen every single time I drink coffee, but it can definitely sneak up on me if it hits me wrong.

High blood pressure

If I ever get a blood pressure reading that is on the high side, I’ve noticed it coincides with excess coffee consumption, which isn’t a huge shocker based on the studies looking at blood pressure and CYP1A2 “slow” genotypes I cited above.

Histamine liberator

This is an obscure and very nerdy addition to the list, but it’s also an important one. For those of us who may not do as good of a job clearing histamine, coffee can cause anxiety and symptoms of allergy to worsen. Why?

It’s rumored to be a substance that “liberates” histamine, meaning our immune cells release histamine as they encounter that delicious black water. If you are one of the millions of Americans sensitive to histamine, this can be a big problem.

The bottom line

The bottom line is that I love coffee and I will continue to have a cup or two a few times a week. However, weeks of regular coffee or espresso every day, multiple times a day, don’t seem to work for me.

The revelation that caffeine has a quarter life was a game changer. I realized that slow metabolizers may have caffeine active in their system for 16 or more hours in a day, which really opened my eyes to the realities of caffeine and sleep for some of us.

Turns out coffee is really “good for you.”

Until it isn’t.

John O'Connor

John O'Connor is the founder of Gene Food, a nutrigenomic startup helping people all over the world personalize nutrition. John is the host of the Gene Food Podcast and a health coach trained at Duke's Integrative Medicine Program. Read his full bio here.

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  1. Ricardo Barrera says:

    I hope you write more about coffee qua histamine liberator. I googled it, but didn’t get informative results.

    • I know, this is a tough one. It gets thrown around a lot that coffee is a histamine liberator, but there seems to be a lack of hard data to prove it. This is why I threw it in, but said “rumored to be” a histamine liberator. This study in rats appears to be the best one out there and shows that caffeine is a fairly potent histamine liberator in animal models:

      • Mark Painter says:

        Coffee is the canary in the coal mine. Following a day of eating foods I knew from experience to cause histamine issues for me, such as unrefined coconut oil or white vinegar, (which sometimes might not even trigger any discernible sxs at the time of consumption) my morning coffee would almost immediately provoke itching over most of my upper torso. Coffee seems to metaphorically bump the full histamine bucket.

  2. Mark, what a great comment. For many of us, and probably the majority of us, the greatest benefit from caffeine comes by staggering doses. I am 100% with you. Your weekend strategy sounds great. I am reserving my coffee days for every so often on the weekend and on the days I record the podcast as I love getting the old “kick” that I used to get when first drinking coffee. At the end of the day, why even drink caffeine every day if the benefits are no longer there? Like you I only get real benefit from coffee when I drink it once or twice a week. Would rather have that one Superman day than 7 straight maintenance days. I also find that once I am detoxed, the occasional decaf espresso from a nice coffee shop is good for the weekdays.

    • Mark Painter says:

      John, you gave me a great idea. Just ordered some green Bali Hai Organic Decaf Indonesia Blend beans!

  3. Mark Painter says:

    I completed my own coffee detox 3 weeks ago after years of progressively stronger and stronger daily dosing. Roasting some green organic beans, 48-72 hours of de-gassing, fine grinding 13-14 grams of beans, 9 ounces of filtered water in with my beloved Italian made espresso maker yielding 8 ounces of liquid black gold became an albatross. The first 3 days or so of cold turkey left me clearly cognitively impaired, sleepy, constipated, and with a headache that started at my crown and ended at my chin. I stayed 100% off all caffeine for 13 days.
    Happy to report now that apparently my adrenal response has recovered as poopage is achieved without benefit of any morning java and cognitive function is equal to what I enjoyed with morning coffee. I have a cup Saturday morning and Sunday morning….and good lord is it wonderful! Was finishing it just as I started reading this blog post. For the first time in more than a decade I get the substantial mood and cognitive processing boost from coffee that hooked us all in the very beginning of our coffee love affair but slipped away so quickly only to leave us feeling just less sleepy in the morning but dependent on the stimulation.

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