The clinical course of patients with cystic fibrosis (CF) is variable and probably determined by many interacting factors. We aimed to examine the influence of early social and clinical factors on long-term survival. A case-control study of adult CF patients was used to compare long-term survivors (aged ≥ 40 yrs) with patients who died before reaching 30 yrs of age. Each case (n = 78) was matched by birth date with at least one control (n = 152), after exclusion of "late diagnosis" patients. Probability-weighted logistic regression models were used to identify influences on survival. Factors resulting in increased probabilities of survival included high body mass index (OR 1.76, 95% CI 1.40-2.22), forced expiratory volume in 1 s (OR per 5% increase 1.54, 95% CI 1.32-1.80), and forced vital capacity (OR per 5% increase 1.54, 95% CI 1.33-1.78) at transfer to the adult clinic and the exclusive use of oral antibiotics (OR 8.31, 95% CI 3.02-22.88). Factors resulting in decreased probabilities of survival were Pseudomonas aeruginosa acquisition (OR 0.18, 95% 0.05-0.65) or pneumothorax before transfer to the adult clinic (OR 0.02, 95% CI 0.004-0.08) and referral from a paediatric clinic in a deprived area (OR 0.13, 95% CI 0.04-0.38). Long-term survival is associated with the clinical features present by the time of referral to an adult clinic. Even "early-diagnosis" disease appears to have different phenotypes, possibly independent of CF gene function, that have different survival patterns.