If you're trying to use a DNA test for health analysis rather than ancestry — to get personalized supplement recommendations, understand how your body processes nutrients, or make sense of genetic variants you've heard about — you've probably run into a version of the same question: does it matter which test you took? Is 23andMe better for health? Does AncestryDNA raw data work for the same things?
The short answer is that both tests work, both raw data files contain the health-relevant variants that matter for supplement analysis, and if you already have one of them, you almost certainly don't need to retest. The longer answer involves some real technical differences that are worth understanding — not because they change the bottom line for most people, but because understanding why both work (and where the minor differences are) helps you use your data with more confidence.
This article gives you an honest, technical comparison of 23andMe and AncestryDNA from the perspective of health analysis, not ancestry. We'll cover how both chips work, which health variants each covers reliably, where 23andMe has a genuine edge, and what to do depending on what you already have.
How Both Tests Actually Work
Neither 23andMe nor AncestryDNA sequences your full genome. Both use what's called a SNP microarray — a chip-based genotyping technology that checks hundreds of thousands of specific, pre-selected positions in your DNA for known variants. Each position is a single nucleotide polymorphism, or SNP (pronounced "snip"). At each SNP, you carry one of a small number of possible letter combinations, inherited from your parents.
Both companies primarily use Illumina chips — the industry standard for consumer genotyping. The current generation of chips used by both tests typically covers somewhere in the range of 600,000 to 700,000 SNPs. That sounds like a lot, but it represents a small fraction of the roughly 4–5 million common variants in the human genome, and an even smaller fraction of your three billion total base pairs. The chips aren't random, though. The SNPs selected for genotyping arrays are chosen because they're well-studied, because they're informative about ancestry patterns, or because they have known associations with health traits and conditions.
The raw data file you can download from either service is a plain text file listing every SNP that was tested, along with your genotype at each position. It's the same format either way: an rsID (a standardized identifier like rs1801133), a chromosome, a position, and two letters representing the alleles you carry. This file is what third-party analysis services — including Whole Gene Health — work with when generating a health report.
Where 23andMe Has a Genuine Edge
23andMe has invested more deliberately in the health side of its chip design than AncestryDNA has. This makes sense given their product history: 23andMe has been offering health reports since the early days of the service, and they've gone through multiple rounds of FDA scrutiny that forced them to be precise about which variants they test and how they report on them. That history shaped their chip selection in ways that matter.
Specifically, 23andMe tends to have better coverage of certain health-associated variants that fall outside the standard ancestry-informative SNPs. Their chip includes more positions relevant to pharmacogenomics (how your body processes drugs), more variants associated with medication metabolism, and better representation of some rarer but clinically meaningful variants in genes like BRCA1/2 and APOE. For users who want to go deep into medication interactions or rare disease risk, this additional coverage is real.
23andMe also has FDA authorization for a specific set of health reports — covering things like carrier status for certain genetic conditions, APOE status for Alzheimer's risk, and a handful of other findings. This FDA authorization process required them to validate the accuracy of their genotyping calls for those specific variants to a clinical standard. It doesn't mean their chip is more accurate overall, but it does mean certain high-stakes variants have been independently verified.
For the subset of users interested purely in clinical-grade variant calling on a small number of high-stakes SNPs, 23andMe's regulatory track record offers some additional confidence.
Why AncestryDNA Raw Data Works Fine for Supplement Analysis
Here's the practical reality: the variants that matter most for supplement optimization — the 100 to 200 well-studied SNPs covering methylation, detox pathways, vitamin metabolism, neurotransmitter regulation, and inflammation — are almost entirely drawn from the standard set of Illumina chip variants that both companies test. These aren't obscure positions. They're among the most studied SNPs in nutritional genomics and functional medicine. Any modern genotyping chip designed for consumer use will include them.
The key genes for supplement analysis — MTHFR (C677T and A1298C), COMT (Val158Met), APOE, VDR (the vitamin D receptor), the CYP enzyme family, MTR and MTRR for the B12 cycle, MAOA and MAOB for neurotransmitter metabolism, inflammatory markers like TNF-alpha and IL-6, and cardiovascular variants like F5 (Factor V Leiden) — are all present and reliably called in both AncestryDNA and 23andMe raw data files.
AncestryDNA's chip has historically been more oriented toward ancestry informative markers, which means their specific SNP selection is somewhat different from 23andMe's. But because both chips cover such a large number of positions and both use well-established Illumina chemistry, the overlap on health-relevant variants is extensive. In practice, analyzing an AncestryDNA raw file for supplement needs produces the same depth of useful findings as analyzing a 23andMe file.
If you've taken AncestryDNA and you're wondering whether you need to buy a 23andMe kit just to access health analysis, the answer is almost certainly no. Your data is already there. Use it.
The Key Health Variants: What Both Chips Cover
To make this concrete, here's a look at the major variant categories relevant to supplement analysis and how both chips handle them:
Methylation: MTHFR, MTR, MTRR
MTHFR C677T (rs1801133) and MTHFR A1298C (rs1801131) are probably the most talked-about health SNPs in functional medicine. Both are on every major consumer genotyping chip. They're present in both 23andMe and AncestryDNA raw data files and are called with high reliability. The same goes for MTR (rs1805087) and MTRR (rs1801394), the two other key methylation cycle genes. All four are standard, well-studied SNPs with extensive published literature and reliable genotyping.
Neurotransmitters: COMT and MAOA
COMT Val158Met (rs4680) is another variant that appears on both chips without exception. MAOA variants (particularly rs6323) are also reliably present. These are high-frequency, well-characterized SNPs that have been on genotyping arrays for years. Neither test will be missing these.
Vitamin Metabolism: VDR and GC
Multiple VDR variants — including BsmI (rs1544410), FokI (rs2228570), and TaqI (rs731236) — are covered by both chips. GC (the vitamin D binding protein gene) variants are similarly present. Vitamin D metabolism is one of the most practically useful areas of nutrigenomics, and both datasets support a thorough analysis.
Detoxification: CYP Enzymes
This is one area where 23andMe's health focus gives it a more consistent edge. CYP enzyme coverage — particularly for CYP2D6, which is highly polymorphic and relevant to medication metabolism — is more complete in 23andMe's chip design. For pure supplement analysis, most CYP1A2, CYP1B1, and basic CYP2C19 variants are covered by both. For pharmacogenomics (medication dosing and interaction analysis), 23andMe's broader CYP coverage is a meaningful advantage.
Cardiovascular and APOE
APOE genotyping (the E2/E3/E4 classification) is available from both services. 23andMe now includes it in their direct-to-consumer reports with FDA authorization; AncestryDNA does not surface it in their interface but the underlying SNPs are present in the raw data and can be analyzed by third-party services. Factor V Leiden (rs6025) is similarly present in both raw datasets.
What Neither Test Can Do
It's worth being clear about the ceiling here. Both 23andMe and AncestryDNA use genotyping arrays, not whole-genome sequencing. That means they only check pre-selected positions — they don't read your entire DNA. If a health-relevant variant exists at a position that wasn't included on the chip, it won't appear in your raw data.
Clinical-grade whole-genome sequencing (WGS) reads every position in your genome and will catch variants that microarrays miss. It's also significantly more expensive — typically $300 to $500 or more for clinical-quality sequencing, versus $99 for a consumer DNA kit on sale. For the overwhelming majority of people, the tradeoff doesn't make sense: the 100 to 200 well-characterized, supplement-relevant variants covered by consumer chips represent the actionable findings that current nutritional genomics research supports. Whole-genome sequencing adds enormous data volume but very little additional practical guidance for supplement optimization.
The variants that matter for methylation support, vitamin D dosing, neurotransmitter balance, and inflammation management are well-established, well-studied, and present on both chips. That's the relevant universe. Consumer DNA kits are genuinely adequate for this purpose.
A Note on Data Privacy
Both 23andMe and AncestryDNA have faced questions about data privacy and the security of genetic data stored in their systems. 23andMe in particular experienced a significant data breach in late 2023, and its subsequent bankruptcy filing in 2025 raised fresh concerns about what would happen to its genetic database. AncestryDNA has faced its own questions about third-party data sharing and law enforcement requests.
The safest approach with either service is the same: download your raw data file, store it locally, and treat your genetic data as you would any sensitive personal information. Once you have the file, you don't need to keep your data in either company's cloud for health analysis purposes. Third-party analysis services like Whole Gene Health work with the file you upload directly — your data is processed for your report and is not retained in a database tied to your identity.
This is true regardless of which test you took. The value of your genetic data is in the file you own, not in an account that a company can access, sell, or lose in a breach.
If You Have Neither Test: Which Should You Buy?
If you're starting from scratch and your primary goal is health analysis, 23andMe is the better default. The reasons are straightforward: their chip was designed with health variants in mind, their health report interface gives you some immediate value even before uploading raw data anywhere, their FDA-authorized reporting on certain variants adds a layer of validated quality control, and their CYP enzyme coverage is more complete for anyone interested in medication interaction analysis.
Both services run regular sales, and both are frequently available at around $99. At that price point, 23andMe's health-focused chip design is worth choosing if you're deciding between them specifically for health purposes.
If your interest is primarily ancestry and you want health analysis as a secondary benefit, either test works fine. AncestryDNA has a larger database and is generally considered stronger for building out family trees. If you already have AncestryDNA, as millions of people do, there is no reason to spend another $99 on 23andMe to run a supplement analysis.
How to Download Your Raw Data
The process is straightforward for both services, though it's not prominently advertised by either.
For 23andMe: log into your account, go to Settings, find the "23andMe Data" section, and click "Download Raw Data." You'll confirm your identity by entering your password and verifying via email. The download is a compressed file containing your complete genotype data.
For AncestryDNA: log into your Ancestry account, go to the DNA section, click on your test results, then look for "Settings" or the gear icon near your results. From there, find "Download Raw DNA Data." You'll receive an email with a confirmation link, after which the file becomes available to download. Like the 23andMe file, it's a compressed plain text file with the same basic structure.
Save both files in a secure location. They don't expire, they don't change, and you only need to download them once. The same file works with any third-party analysis service that accepts data from that provider.
The Bottom Line
The 23andMe vs. AncestryDNA question has a clear practical answer: use what you have. Both raw data files contain the variants that matter for supplement analysis. The technical differences between the two chips are real but minor for most health-focused use cases. 23andMe's health-specific chip design and FDA-authorized reporting give it a modest edge, particularly for CYP enzyme coverage and pharmacogenomics. But AncestryDNA raw data fully supports a complete analysis of methylation, vitamin metabolism, neurotransmitter genetics, inflammation, and cardiovascular variants.
If you've been sitting on an AncestryDNA test because you assumed it wasn't useful for health analysis, it's time to download your raw data and put it to work. If you're buying a test for the first time and health is your priority, go with 23andMe. Either way, the data you end up with is the starting point for something considerably more useful than ancestry pie charts.
The genes that determine how your body processes folate, responds to vitamin D, clears neurotransmitters, and manages inflammation don't care which company's chip read them. What matters is that the data is accurate, the variants are present, and someone knows what to do with them.