Three Million Reasons South Africa Needs a Rare Disease Policy

By Kelly du Plessis, Founder & CEO, Rare Diseases South Africa

For thirteen years, I have watched South African families walk the same lonely road: a child who isn't developing quite right, a specialist out of ideas, a referral letter that goes nowhere, years, sometimes a decade, before anyone can put a name to what's wrong.

We at Rare Diseases South Africa (RDSA) have always known this journey is common. What we haven't had, until now, is a number.

We have one now. And it's a big one.

A new study, Breaking Down the Burden of Rare Diseases in South Africa, commissioned by the Rare Disease Access Initiative and funded by the Innovative Pharmaceutical Association South Africa, has just delivered the first evidence-based, national-level estimate of how many South Africans live with a rare disease. Published in the Orphanet Journal of Rare Diseases, the study applied a globally validated methodology, built on the Orphanet database of more than 6,000 conditions, to our own population statistics for the first time.

The headline figure: an estimated 3,030,204 South Africans, roughly 4.8% of the population, are living with one of the 3,728 rare diseases included in this analysis. That's not a rounding of the old "6 to 8% of any population" rule of thumb we've relied on for years, the one that produced a vague guess of 4.2 million. This is a number built from South African population data, disease by disease. And because the study could only include the subset of rare diseases with usable prevalence data, and had to exclude rare cancers, infections and toxin-related conditions entirely, even 3 million is almost certainly an undercount of the true picture.

Tellingly, this study didn't happen in a vacuum. It exists because the National Department of Health itself asked for it, in a direct request. They essentially requested a more granular breakdown of a burden everyone suspected was large but nobody could prove.

A few findings should change how everyone including government, funders, clinicians, and the public, think about rare disease in this country.

1. The burden is concentrated. Just 404 conditions, barely 11% of those studied, account for 98% of every affected South African. That's not a reason to ignore the other 3,300-plus conditions; but it's a gift to policymakers. It means a focused investment in diagnosing and managing a defined, manageable list of conditions would change life for the overwhelming majority of rare disease patients in this country. We don't need to solve for 3,728 diseases at once to make a serious dent in this crisis.

   
   

2. This is overwhelmingly a child health issue.77% of these conditions present in childhood, and 31% within the first four weeks of life. A third of children with a rare disease never see their fifth birthday. Every conversation South Africa has about newborn screening, maternal and child health, and reducing under-five mortality is, whether we say it out loud or not, a conversation about rare disease.

   
   

3. More than 1.3 million South Africans are estimated to live with moderate to severe functional disability as a result of a rare disease. This is not a niche clinical curiosity. It is a disability and social-support crisis playing out largely unseen, inside a health system with no coordinated national surveillance for these conditions at all. Our existing congenital disorder registry, running since 2006, is estimated to capture less than 5% of actual cases.

   
   

4. Fewer than 5% of rare disease patients need high-cost medicines. The other 95% need what most of medicine has always needed: an accurate, timely diagnosis and a treatment plan that, for many rare diseases, is a specific diet or a daily low-cost tablet. Phenylketonuria (PKU) is managed with a controlled diet. Congenital hypothyroidism, untreated, causes irreversible developmental damage; treated early, it's a daily dose of a cheap hormone replacement. The myth that "rare disease care is unaffordable" has justified inaction for years. This data says otherwise. It confirms that the small group who do need advanced therapies are being badly failed: of 59 rare diseases with a high-cost drug approved somewhere in the world, only 25 are registered for use in South Africa at all, and only a portion of those are genuinely accessible to patients who need them.

In May 2025, the World Health Assembly adopted a resolution declaring rare diseases a global health priority under the Universal Health Coverage and equity agenda, and it requires member states, South Africa included, to act and report back on progress.

We now have both the international mandate and, for the first time, the local evidence to meet it.

But the authors of this study are honest about its biggest limitation, and it's the one RDSA exists to solve.

These are modelled estimates, the best available application of global data to South African population statistics. They are not, and cannot be, a count of actual South African patients. The study's own recommendations call, explicitly, for "local validation of global estimates via RD registries and clinical surveillance." In other words: the next step in turning this evidence into policy is real South Africans, standing up and being counted.

That is exactly what raregistry.org.za was built to do. It is South Africa's own patient-led rare disease registry. Live, free, and designed from the ground up to ask as little as possible of an already exhausted patient or caregiver. Every person who registers turns one line of a modelled estimate into a documented South African life: their diagnosis journey, their condition, their unmet needs. That is the empirical, local data this report calls for, and it is the data the Department of Health, funders and researchers will need to move from "roughly 3 million, we think" to a health system genuinely built around who is actually here and what they actually need.

If you are living with a rare disease, or caring for someone who is, please register at raregistry.org.za. If you are a clinician, a geneticist, a genetic counsellor, or run a clinic where these patients are seen, please tell them about it. This report gave South Africa a number. Now we need to give that number a face, a file, and a voice loud enough that no policymaker can call rare disease "too rare to matter" again.

Three million South Africans are waiting for a policy that treats their conditions as more than a statistical footnote. The evidence now exists. What we do with it is up to us.

Kelly du Plessis - CEO, Rare Diseases South Africa

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Writer's Note: This report was led by Prof Helen Malherbe, a former director of Rare Diseases South Africa, whose early contributions helped shape this organisation and this movement in South Africa. A study of this scope and methodological rigour represents a significant undertaking, and South Africa's rare disease community owes Helen genuine recognition and gratitude for producing it.