To assess whether vitamin D deficiency is a cause of increased morbidity and mortality or simply an indicator of poor health, we assessed (1) the cross-sectional and longitudinal association of vitamin D deficiency with self-rated health (SRH) and frailty and (2) the association of vitamin D deficiency with mortality, with and without control for SRH and frailty. Analyses were performed in 9,579 participants of the German, population-based ESTHER cohort (age-range at baseline: 50-74 years), with follow-ups after 2, 5 and 8 years (mortality: 12 years). During follow-up, 129 subjects newly reported poor SRH, 510 developed frailty and 1,450 died. In cross-sectional analyses, subjects with vitamin D deficiency had higher odds of a poor SRH and frailty but no association with SRH or frailty was observed in longitudinal analyses. The association of vitamin D deficiency with all-cause and several cause-specific mortalities was strong and unaltered by time-dependent adjustment for classic mortality risk factors, SRH and frailty. In conclusion, vitamin D deficiency may not cause frailty or poor general health but may nevertheless be a prognostic marker for mortality, independent of the individual's morbidity.