Chronic immune diseases are often reported to be on the rise and are speculated to share early life risk factors. Here, we investigated year of birth as a common denominator for time trends using the consistent data source of the Danish National Patient Registry with 35 years nationwide coverage. Observational nationwide birth cohort registry study, where persons born in Denmark since 1953 were investigated for chronic immune diseases per person years at risk. Outcomes were defined by inpatient hospitalizations in pre-chosen age bins by year of birth in 5 year bins. A population of 3.8 million persons born in Denmark since 1953 was investigated for a total sum of 68 million person years in the ages 5–34 years. We found increasing trends by year of birth for juvenile arthritis age 10–14, adult asthma age 20–24, inflammatory bowel diseases age 20–24, and multiple sclerosis age 25–29, whereas type 1 diabetes age 15–19 was declining until birth year mid 1980s followed by a subsequent increase. Childhood asthma age 5–9 inpatient hospitalizations were relatively stable over time. Nationwide introduction of measles, mumps, rubella vaccine in 1987 did not alter the trends. Hospitalization for the chronic immune diseases adult asthma, juvenile arthritis, inflammatory bowel diseases and multiple sclerosis showed a general increasing trend by birth year in recent 35 years while diabetes 1 and childhood asthma seemed stable in this period. These results were not affected by the introduction of vaccinations against the major childhood viral infections.