There are serious limitations inherent to long-term vaccine safety studies as currently implemented. Post-licensure studies on vaccine safety typically employ an “N vs. N + 1” design of analysis, meaning they compare fully vaccinated children with fully vaccinated children missing only one vaccine. Despite reports of increases in vaccine cessation, virtually none of the post licensure vaccine safety studies have included comparisons to groups completely unexposed to vaccines.
A few independent (non-CDC) studies do exist that have compared outcomes between vaccinated and unvaccinated children.
- A small survey study of 415 families with homeschooled children by Mawson et al., 2017  that compared vaccinated with completely unvaccinated children reported increased risk of many diagnoses among the vaccinated children including (condition, fold increase): allergic rhinitis (30.1), learning disabilities (5.2), attention deficit hyperactivity disorder (ADHD) (4.2), autism (4.2), neurodevelopmental disorders (3.7), eczema (2.9), and chronic illness (2.4). The increased risk of neurodevelopmental disorders appeared to be higher in cases of preterm births.
- A study from Germany (Schmitz et al., 2011)  reported no increases in adverse outcomes other than atopy.
A limitation of both of these studies is that they relied on parental surveys, and both had a small unexposed group. A further limitation in the German study  is that they also defined a child as unexposed to vaccines even if they received vaccination for varicella, rotavirus, pneumococcal, meningococcal, influenza, and/or others; the study, therefore, is not “vaccinated vs. unvaccinated”.
Studies of Diphtheria, Pertussis, and Tetanus (DTP) vaccine that had an unexposed group found an increased risk of mortality (Mogensen et al., 2017)  and asthma (McDonald et al., 2008)  in the vaccine exposed group. Gallagher and Goodman, 2008  reported increased ASD in a hepatitis B vaccine-exposed group.
Studies funded by the pharmaceutical industry or conducted by the CDC typically tend to find no harm associated with vaccination, while studies conducted without
pharmaceutical industry funding have often found harm.
Hooker and Miller 2020  recently found an increase in odds ratio (OR) in developmental delay (OR 2.18), asthma (OR 4.49), and ear infection (OR 2.13) in vaccinated children compared to unvaccinated children in a study using data from three practices. – See the post dedicated to the amazing study.