Ranking deficiencies depends heavily on which population and which cutoff you use, so treat any "top three" list as approximate. That said, three nutrients appear consistently across datasets: iron, vitamin D, and vitamin B12.
Iron
NIH ODS states that iron deficiency "is not uncommon in the United States, especially among young children, women of reproductive age, and pregnant women," and links it to poor diet, malabsorptive disorders, and blood loss. Menstrual blood loss is a structural reason the burden falls unevenly by sex.
Vitamin D
Prevalence depends entirely on the threshold chosen, which is why estimates vary so widely. USPSTF cites NHANES 2011–2014 data using mass spectrometry, noting the prevalence varies based on how deficiency is defined.
NIH ODS explains that the Food and Nutrition Board considers 50 nmol/L (20 ng/mL) sufficient for most people, with deficiency risk increasing below 30 nmol/L (12 ng/mL) — and notes that levels associated with deficiency "have not been definitively identified."
Vitamin B12
B12 deficiency concentrates in specific groups rather than the general population. NIH ODS reports that between 3% and 43% of community-dwelling older adults are deficient depending on the definition used, and that atrophic gastritis affects 2% of the general population but 8–9% of adults aged 65 and older.
What the ranking does not tell you
Population prevalence says nothing about an individual. Being in a low-prevalence group does not exclude deficiency, and being in a high-prevalence group does not establish it. What matters for you personally is your own combination of diet, medications, absorption, and symptoms.
Our free assessment works through those individual factors rather than population averages.
References
This article summarizes published guidance from the sources linked above. It is general information, not medical advice, and it cannot tell you whether you personally have a deficiency. Only a clinician ordering the right test can do that. If you have symptoms that concern you, speak to a doctor.